Biophysics of Systems – Übersicht

3 x 3/4hour lecture + 1 hour seminar

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Only for Master Students

Background in Biophysics strongly recommended

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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:

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