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Biophysics of Systems (Master) – Übersicht

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Informationen zur Vorlesung

Zeit und Ort

Tuesday 10.15 - 13.30
Kleiner Physikhörsaal (N020)

We will explore evolution, pattern formation, embryogenesis, biochemical networks, chemotaxis, gene regulation, high throughput methods, neural networks and game theory. (3 hour lecture, 1 hour seminar, 6 Credit Points, Only lecture: 4 credit points)

For Master students, background on Cellular Biophysics, Molecular Biophysics and Theoretical Biophysics highly recommended. Lecture within the Biophysics Program of the Physics Master

                >>>>>> Biophysics Lab Course <<<<<<<

3.5. Introduction to Systems Biophysics (Intro Slides, Seminar Prep)

Introduction to Lecture. Presentation of Seminar Topics (decision on the topics next week)
                  >>>   [Seminar Papers as ZIP-File: Paper1-7, Paper8-15  [update 30 Mai]]  <<<<
Contact: Mario Herzog and Maren Funk

Journals via the Regensburg Link

Peek into Science: Talk of Dr. Carsten Rohr from 12-13h with Pre & Postdiscussion


10.5. Evolution Part 1 (Intro Slides, Main Slides)

Darwin and the phyolgenetic tree. Common strategies of life. Early evolution. Timeline of evolution. Chemical evolution: building blocks. Places for the origin of life. Hydrothermal chemistry. Decision on the Seminar speakers.

Peek into Science: Talk of Dr. Jörn Dunkel from 12-13h with Pre & Postdiscussion


17.5. Evolution Part 2 (Add. Slides)

Hydrothermal chemistry. Achaea. Hydrothermal accumulation. Convective PCR. Population Dynamics. Limited growth. Competition for food. Predator-Prey model. Eigen-Model of Molecular evolution. Error threshold. Oxygen crisis. Endosymbiotic development of eucaryotes.

Seminar: The Spiegelman Monster (#2 Christian Schwall)

Peek into Science: Talk of Prof. Gašper Tkačik from 12-13h with Postdiscussion


24.5. Gene Regulation and stochastic effects in regulatory networks (Evo2, Gene Regulation, Noise)

Basics, Lac Operon, Boolean networks, Intrinsic and extrinsic noise
Seminar 2:
The basic reproductive ratio of life (#12 Ulrich Lichnovsky  & Maksim Greiner)
Single-molecule fluorescence spectroscopy of Proteins (#1 Stefan Holler & Franz Englbrecht)

31.5. Pattern formation (Slides 1, Slides 2, Slides 3)

Biological pattern formation and morphogenesis. Activator-Inhibitor models. Structure formation in space and time. Oscillating reactions. Hydra. Embyrogenesis.

Seminar: A synthetic Oscillator in a Living Cell (#3 Lothar Maisenbacher & Benedikt Ludwig)

7.6. Neural Networks (Slides)

Basics Models and physiological Basis of Neural networks

Seminar:
Molecular Crowding: does it have an effect? (#4 Alexander Pirner & Marc Reuthern)

14.6. Pfingstdienstag: no lecture

21.6. Bacterial Chemotaxis (Slides, Connection to Neural Networks)

Locomotion of E-Coli, directional movement, run and tumble, Che-Protein network, adaptation, Sensitivity, Cooperative Binding, Hill equation, Konformation model of receptor, Ising model of receptor field, Boolean Algebra within receptor fields.

Seminar:
Evolution in Fitness Landscapes (#5 Katharina Nekolla & Eva-Maria Roller)
Approaches using cell free systems (#6 Marco Meixner & Timo Hanke)

28.6. Chemotaxis of Eukaryotes (Slides)

Chemotaxis of Dictyostelia. Outlook: Chemotaxis in Brain development.

Seminar:
Evolution of indirect reciprocity (#10 Jürgen Stephan, Max Brunner & Lars Kleemeier)

Science in progress: The eusociality fight (#11 Hao Wu & Lizhe Liu)

5.7. Regulation using RNA: Splicing, RNA folding, Interference RNA (Slides)

Seminar: RNA Folding used as a switch (#7 Anita Ladenburger Valentin Stierle)

mRNA, RNA-interferenz, siRNA in medicine, splicing, spliceosome

Seminar: Entropically driven DNA machines (#14 Johanna Schappert)

12.7. High Throughput Methods and Synthetic Biology (Slides1, Slides2)

Experimental foundations, overview over different methods

Seminar:
Molecular cut & paste (#8 Matthias Hiermaier & Georg Urtel)
Third Generation Sequencing (#13 Mari Gorelashvili. Claas Reckmeier)
Peek into Science: Talk of Dr. Thomas Surrey from 12-13h with Postdiscussion

19.7. Game theory and evolution (Slides)

Description of economic processes, application in population dynamics

Seminar: Some like it hot: Biomolecule binding quantified with thermal fields (#9 Simon Mates & Ediz Sariisik)

26.7. Oral exam:

Starting 10.15 in 10 minutes intervals in Room NU113, below kleiner Physikalische Hörsaal. Participant list and exam times:

Name Prüfungszeit
Valentin S. 10.15
Ulrich L. 10.25
Timo H. 10.35
Stefan H. 10.45
Simon M. 10.55
Max B. 11.05
Matthias H. 11.15
Mari G. 11.25
Marco M. 11.35
Marc von R. 11.45
Maksim G. 11.55
Lothar M. 12.25
Lizhe L. 12.35
Lars K. 12.45
Anna Katharina N. 12.55
Jürgen S. 13.05
Johanna S. 13.15
Hao W. 13.25
Georg U. 13.35
Franz E. 13.45
Eva-Maria R. 13.55
Ediz S. 14.05
Claas R. 14.15
Christian S. 14.25
Benedikt L. 14.35
Anita L. 15.05
Alexander P. 15.15
Alexander M. 15.25

Verantwortlich für den Inhalt: Dieter Braun