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Biophysics of Systems – Übersicht

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Lecture and Seminar in the Biophysics Program in the Physics Master

Informationen zur Vorlesung

Zeit und Ort

Thursday 14.15-17.15
Schellingstr. 4, 2nd Floor, 206
First Lecture at 22.10.

3 x 3/4hour lecture + 1 hour seminar


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Only for Master Students

Background in Biophysics strongly recommended

---------------- 6 CP ----------------


Lecture within the Biophysics Program of the Physics Master

Details of the Biophysics Program here

 

22.10. Introduction

Overview over Systems Biophysics

Tutorial: What do we expect from a good seminar talk?

Presentation of Seminar Topics (decision on the topics next week)

Paper of Seminars as ZIP-File (old version)

Paper of Seminars (update of 27.10.)

 

29.10. 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.


5.11. 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 1: Q-beta replicase: The Spiegelman-Monster (Felix Segerer)

Literature: Spiegelman-PNAS Paper und Eigen-Review



12.11. Pattern formation (Part 1, Part 2)

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


Seminar 2: Gierer-Meinhardt Model (Magnus Schwörer)

Sackmann-Skript Kap.III(23), Gierer-Meinhardt Model on Scholarpedia

(future: Hydra)

19.11. Introduction to biochemical networks

Enzyme kinetics. Michaelis Menten. S-Systems.


Seminar 3: Single-Molecule Enzymatic Dynamics (Elke Hebisch)

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



26.11. Bacterial Chemotaxis

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 with receptor fields.


Seminar 4: Konvektive PCR und hydrothermale Akkumulation

Literatur: Convective PCR (PRL), Hydrothermal Accumulation (PNAS) and Evolution (Physical Biology)


3.12. Chemotaxis of Eukaryotes
Chemotaxis of Dictyostelia. Outlook: Chemotaxis in Brain development.

Seminar 5a: Intracellular Kinetics and Molecular Crowding

Literature: LockIn Imaging of Cell Kinetics + Ellis: Macromolecular crowding: obvious but underappreciated

Seminar 5b: Controlled Evolution of Ecoli (Fabienna Arends)

Literature: Tans et.al. (2007)

10.12. Wdh.: Chemotaxis of Eukaryotes
Chemotaxis of Dictyostelia. Outlook: Chemotaxis in Brain development.

 

Seminar 6a: Synthetic Networks in Bacteria: Repressilator (Sebastian Gude)

Literature: Elowitz & Leibler (2000)
Seminar 6b: Bacteria in Microfluidic Habitat

Literature: Austin et.al. (2003)



17.12. Gene Regulation (Part 1, Part 2)

Lac Operon, boolean networks


Seminar 7a: Neurons are optical fibers in the eye (Kien Nguyen)

Literature: Guck et.al. (2007)

Seminar 7b: Cell free extracts as model cells (Arne Hartz)

Literature: Noireaux et.al. (2006)



7.1. Regulation based on RNA (Part 1, 2,3)

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


Seminar 8a: RNA as Switch (Arne Hartz)

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

Seminar 8b: Bacteria Subtilis: an excitable System (Peter Röttgermann)

Literature: Elowitz (2006)

14.1. Stochastic effects in regulatory networks (Part 1, Part 2)

Intrinsic and extrinsic noise, quorum Sensing. [Collins (2005); Ellowitz et. al (2002)]


Seminar 9a: Introduction to modern biophysics in the NanoSystems Initiative Munich (NIM) (Sebastian Gude)

Literature: Websites of NIM scientists
Seminar 9b: Mass Spectrometry in Proteomics

Literature: Reviews


21.1. High Throughput Methods of Systems Biology (Part 1, Part 2)

Experimental foundations, overview over different methods (see Seminar)


Seminar 10: Measurement Methods in Immunology (Astrid Zeder)
Literature: pages 186-203 of "Der Experimentator: Proteinbiochemie, Proteomics"


28.1. Neuronal Nets (PDF)

Theoretical and real neuronal networks (Visitor: Andreas Herz)


Seminar 11: Phase Locked Neuronal Networks (Christian Winnerlein)

Literature: van Hemmen - Papers (PDF und im Buch Models of Neural Networks II)

 


4.2. Game theory and evolution (PDF)

Description of economic processes, application in population dynamics


Seminar 12: Diversity in a diffusive Scissors-Game (Philip Wolf)

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

 


11.2. Prüfungen
15-minute Oral exams:

Name Time
Astrid Zeder 14.15
Felix Segerer 14.30
Elke Hebisch 14.45
Arne Hartz 15.00
Peter Röttgermann 15.15
Magnus Schwörer 15.30
Philip Wolf 15.45
Christian Winnerlein 16.00
Fabienna Arends 16.15
Francesca Bisello 16.30
Sebastian Gude 16.45

You can obtain the "Scheine" in the Braun lab.

Verantwortlich für den Inhalt: Dieter Braun