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Biophysics of Systems (Master) – Übersicht

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Informationen zur Vorlesung

Zeit und Ort

Monday 12.30 - 16.00
H 537, Schellingstr. 4, 5th floor

We will explore evolution, pattern formation, embryogenesis, biochemical networks, chemotaxis, gene regulation, high throughput methods, neural networks, game theory and econophysics of money. Lecture will include a short introduction in modeling of chemical networks with MatLab and reaction-diffusion systems with Comsol. (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

6.10. Introduction to Systems Biophysics

From Evolution to (Synthetic) Biology. Introduction to the topic and the lecture.
Presentation of Seminar Topics (decision on the topics next week)
>>>  [Seminar Papers as ZIP File (rename after download to NN.pdf.tar.gz)]  <<<

13.10. How all began: the Origin of Evolution Part 1 (PDF of Part 1 and 2)

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 slots and speakers.

20.10. How all began: the Origin of Evolution Part 2 (updated PDF of Part 1 and 2)

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:
#02 Survival of only the Shortest: Spiegelman (Alexander Borowac)
#05 Driving the origin of life with a temperature gradient: Replication Trap (Martin Tosstorff)

27.10. Bacterial Chemotaxis (Slides, Movie 1,2,3,4)

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:
#23 How to get long RNA: Polymerization Trap (Markus Petermann)
#08 Microscale Thermophoresis: Some startup like it hot (Sophia Schaffer)

3.11. Chemotaxis of Eukaryotes (Slides, Growthcones)

Chemotaxis of Dictyostelia. Outlook: Chemotaxis in Brain development.
Seminar:
#06 Translation in a bubble: towards creating synthetic cells (Thomas Rind)
#03 Repressilator: how to make an oscillator with DNA, RNA and Proteins in a bacteria (Alina Fedorchuk)

10.11. Modeling of chemical Networks (+Matlab introduction)

Introduction to the modelling of reaction networks, starting from simple examples to more complex models. Simulations will be programmed in Matlab, with the possibility to program examples yourself with your notebook.
Seminar:
#11 When every molecule counts: stochastic metabolism in single cells (Laura Lechtenberg)
#13 Cause of the jet-lag: the mamalian circadian rhythm (Benjamin Alerisch)

17.11. Embryogenesis and Pattern formation (Slides 1,2,3)

Biological pattern formation and morphogenesis. Activator-Inhibitor models. Structure formation in space and time. Oscillating reactions. Hydra. Embyrogenesis.
Seminar:
#17 The embryo as laboratory: using developmental processes (Tobias Andres)
#14 Where the patterns and arms come from: Spatial transcription in the Embryo (Johannes Gebhard)

24.11. Modeling of Reaction-Diffusion Systems (+Comsol introduction)

Introduction to the finite element modelling of reaction-diffusion systems with examples from Embryogenesis and reaction oscillation systems. Simulations will be programmed in Comsol, with the possibility for hands on programming on your notebook.
Seminar:
#01 Single molecule spectroscopy (Ulrich Schwarz)
#09 The mechanism of single proteins: Single Molecule Enzymatic Dynamics (Philipp Lorenz)

1.12. Gene Regulation and stochastic effects in regulatory networks (Slides 1 2 3)

Basics, Lac Operon, Boolean networks, Intrinsic and extrinsic noise
Seminar:
#21 Listening to the protein production of single cells with RNA seq (Pablo M.)
#07 Sequencing at the single molecule level (Andriy Goychuk)

8.12. Regulation using RNA: Splicing, RNA folding, Interference RNA (Slides 1 2 3)

mRNA, RNA-interferenz, siRNA in medicine, splicing, spliceosome
Seminar:
#18 RNA interference in the clinic: overview over the state of the art (Leonard Schendel)
#22 The role and mechanics of nucleosome positioning (David Heider)

15.12. Neural Networks (PDF)

Basics Models and physiological Basis of Neural networks
Seminar:
#10 Phase locking: how networks can encode patterns in the time domain (Jatin Talwar)
#24 Optogenetics - how to use light to manipulate neuronal networks (Alexandra Götz)

22.12. High Throughput Methods and Synthetic Biology (Slides 1 2)

Experimental foundations, overview over different methods
Seminar:
#20 Get the sequence fast: newest sequencing methods (Benedikt Schlederer)
#12 Sequencing on the single cell level (NN)

12.1. Game theory and evolution (Slides)

Description of economic processes, application in population dynamics
Seminar:
#15 Iterated Prisoners Dilemma: how repetition changes a game (Robert Lohmeyer)
#04 Scissors, Rock and Paper on the molecular scale and the role of diffusion (Marc Eppler)

19.1. Physically motivated models of monetary exchange

Introduction to concepts of econophysics applied to the exchange of goods between subjects. Random exchange models and their (dis)ability to memorize past exchanges.
Seminar:
#16 The rare cases of combinatorics in communication and the special case of language (Julian Stein)
#19 How to find pharmaceutical compounds: the ins and outs of fragment screening (Alexandra Fink)

26.1. and 2.2. Oral exams:

Starting 13.00 - 17.00 the Mo 26. Jan and at 10.00 - 15.00 the Mo 2. Feb in 15 minutes intervals we will have oral exams in Room NU113, below the "kleiner Physikalische Hörsaal". Topic of the exam is the lecture and the talks.

Slots for the oral exams:

Monday 26. Jan

Laura Lechtenberg 13:30

David Heider 13:45

Markus Petermann 14:00

Thomas Rind 14:15

Alex Götz 14:30

Alexandra Fink 14:45

Benjamin Aleritsch 15:00

benedikt Schlederer 15:15

Talwar Jatin 15:30

Alina Fedorchuk 16.00

 

Monday 2. Feb.

Sophia Schaffer 10:30

Leonard Schendel 10:45

Alexander Borowac 11:00

Andriy Goychuk 11:15

Julian Stein 12:00

Martin Tosstorff 12:15

Marc Eppler 12:30

Verantwortlich für den Inhalt: Dieter Braun