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Biophysics of Systems – Übersicht

  • Übersicht

Lecture and Seminar in the Biophysics Program for the Physics Master.

Informationen zur Vorlesung

Zeit und Ort

Tuesday 10.15 - 13.45, Kleiner Physikhörsaal

We will explore the 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)

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

20.4. Introduction

Overview over Systems Biophysics, Introduction to Evolution

What do we expect from a good seminar talk?
Presentation of Seminar Topics (decision on the topics next week)
Seminar-Papers as ZIP. Kontakt: Hubert Krammer and Christof Mast
Link to Journals and Paper-PDFs through LMU Login

27.4. Evolution Part 1 (PDF)

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.


4.5. Evolution Part 2 (PDF)

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 1a: Q-beta replicase: The Spiegelman-Monster (N.N.)

Literature: Spiegelman-PNAS Paper und Eigen-Review


11.5. Gene Regulation and stochastic effects in regulatory networks (Slides 1,2,3,4)

Basics, Lac Operon, Boolean networks, Intrinsic and extrinsic noise

Seminar 2a: Cell free extracts as model cells  (Severin Schink)
Literature: Noireaux et.al. (2006)
Seminar 2b: Synthetic Networks in Bacteria: Repressilator (Sandra Diefenbach)
Literature: Elowitz & Leibler (2000)

18.5. Pattern formation (Stochastic Expression + Switches 1,2; Pattern Formation 1,2,3)

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

Nicht ganz ernster Youtube-Hydra-Link


Seminar 3: Morphogenesis of Hydra (Johannes Frohnmayer)


25.5. Pfingstdienstag ist vorlesungsfrei


1.6. Modelling of biochemical networks (Slides)

Enzyme kinetics. Michaelis Menten. S-Systems.


Seminar 4a: Single-Molecule Enzymatic Dynamics (Simon Holzner)

Literature: Lu & Xie, Science 282, 1877 (1998)

Seminar 4b: Imaging Kinetics in Living Cells to probe Molecular Crowding (Julian Hartmann)

Literature: Schön, Krammer, Braun, PNAS, 106, 21649 (2009)

 

8.6. Bacterial Chemotaxis (Slides)

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 5a: Boolean Algebra within Receptor fields. (Javier Carrillo)

Literature: Papers of Tom Duke

Seminar 5b: Bacteria in Microfluidic Habitat (Ferdinand Breithuth)
Literature: Austin et.al. (2003)

15.6. Chemotaxis of Eukaryotes (Slides)
Chemotaxis of Dictyostelia. Outlook: Chemotaxis in Brain development.

 

Seminar 6: Controlled Evolution of Ecoli (Friederike Möller)

Literature: Tans et.al. (2007)

 

22.6. Regulation using RNA (Growth Cones, Splicing,  RNA folding, Interference RNA)
mRNA, RNA-interferenz, siRNA in medicine, splicing, spliceosome

 

Seminar 7: RNA as Switch (N.N.)

Literature: RNA Switch due to fast cooling, calculation of RNA folding, RNA switch in expression.

 

29.6. High Throughput Methods of Systems Biology (Neural Methods, Parallel Methods of Systems Biology)

Experimental foundations, overview over different methods


Seminar 8a: Bacteria Subtilis: an excitable system (N.N.)
Literature: Elowitz (2006)
Seminar 8b: Biophysics within the NanoSystems Initiative Munich (Sebnem Tuncay)
Literature: Websites of NIM scientists

>>>>>>>>> Important link: Biophysics Lab Course <<<<<<<<<<<<<<<<<<<<<

 

6.7. Game theory and evolution (Game Theory, Spieltheorie, Money Mechanics 1,2)

Description of economic processes, application in population dynamics


Seminar 9: Diversity in a diffusive Scissors-Game (Dominik Thalmeier)

Literature: Reichenbach-Frey-Nature Paper (Nature & PRE)

 

13.7. Oral exams (15 minutes per student)

20.7. Synthetic Biology (Slides, Papers)

Final Marks:

Mat# End

Mark

5290

2.0

3059

1.3

7988

1.0

6457

1.3

7500

2.0

9332

2.3

7099

1.3

5725

1.7

NaN

1.3

 

Verantwortlich für den Inhalt: Dieter Braun