Biophysics of Systems (Master) – Übersicht

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: