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Biophysics of Systems (Master) – Übersicht

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Informationen zur Vorlesung

Zeit und Ort

Wednesday 12.15 - 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

14.10. Introduction to Biophysics of Systems (Slides, requires LibreOffice)

From Evolution to (Synthetic) Biology. Introduction to the topic and the lecture.
Presentation of Seminar Topics - decisions on early Seminar Slots.
>>> [Seminar Papers as tar 51MB] <<<
>>> if above does not work, here as .zip <<<

21.10. How all began: the Origin of Evolution Part 1 (Slides Evolution 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. No Seminar.

28.10. How all began: the Origin of Evolution Part 2 (LabView ODE simulation, Slides Evolution 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: Synthetic cellular System (Noireaux) : Liedl + Aepfelbacher

4.11. 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: Single Molecule Enzyme Dynamics (Sunney Xie) : Gadaili + Banas

11.11. Modeling of chemical Networks (+Matlab introduction) (Zip)

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: Optogenetics in Flies (Anderson) : Arrubarrena + Herraiz

18.11. Chemotaxis of Eukaryotes (Slides, Neural Guidance by chemotaxis, Matlab Code and Paper for cAMP Oscillation)

Chemotaxis of Dictyostelia. Outlook: Chemotaxis in Brain development.
Seminar: Molecular Cut & Paste (Gaub): Kulenkampff + Auer

25.11. Embryogenesis and Pattern formation (Slides)

Biological pattern formation and morphogenesis. Activator-Inhibitor models. Structure formation in space and time. Oscillating reactions. Hydra. Embyrogenesis.
Seminar:
Human Circadian Clock (Takahashi): Mittermeier + Samara
Nucleosome Positioning (Gerland): Servera + Araceli

2.12. High Throughput Methods and Synthetic Biology (Christof) [Slides 60MB!]

Experimental foundations, overview over different methods
Seminar:
Microscale Thermophoresis (Nanotemper Duhr/Baaske) : Gramlich + Kies
Single Molecule Spectrocopy (Hofsken) : Eckermann + Freitag

9.12. 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:
Repressilator:
Oscillator in E-Coli (Leibler) : Niederauer + Dietrich
Fitness Landscapes (Tans): Teves + Wissenberg

16.12. Gene Regulation and stochastic effects in regulatory networks.
Regulation using RNA: Splicing, RNA folding, Interference RNA (Slides, Friederike)

Basics, Lac Operon, Boolean networks, Intrinsic and extrinsic noise
Seminar:
Single Molecule Sequencing (Turner) : Grube + Enrico Ridente
Applying RNA interference: Kilwing + Ober

23.12. Neural Networks (Slides)

Basics Models and physiological Basis of Neural networks
Seminar: no seminar

13.1. Game theory and evolution (Slides Molecular Evolution, Slides Game Theory)

Description of economic processes, application in population dynamics
Seminar:
Iterated Prisoner Dilemma : Matreux+Seebauer
High throughput Sequencing: Manakov + Grimmeißen

20.1. Physically motivated models of monetary exchange (Slides)

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:
Game Theory with Diffusion (Frey) : Ermatov + Deng
Neural Networks: Phase locking (Gerstner) : Baisert

27.1. and 3.2. Oral exams (15 minutes each) [Time table as PDF]
Oral exams are in the Labs of Prof. Braun (NU115, below machine shop)

biophysics

Verantwortlich für den Inhalt: Dieter Braun