Biophysics of Systems (Master) – Übersicht

We will explore the physics of biological systems, including their origin, evolution, pattern formation, embryogenesis, biochemical networks, chemotaxis, gene regulation, high throughput methods, neural networks and game theory. The lecture will include a short introduction to reaction-diffusion systems with Comsol. It is a 3 hour lecture, 1 hour seminar, 6 Credit Points. The lecture is for Master students, open to other discilines and background on Cellular Biophysics, Molecular Biophysics and Theoretical Biophysics is helpful and recommended. Lecture is within the Biophysics Program of the Physics Master.

16.10. Introduction to Biophysics of Systems (Slides 1,2 and Howto Seminar)

From Evolution to (Synthetic) Biology. Introduction to the topic and the lecture.
Presentation of Seminar Topics - Seminar papers with pwd below.

23.10. How all began: the Emergence of Life (Slides)

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.

30.10. Slides 1 2 3 4
6.11. Slides 1 2
13.11. Slides 1 2
20.11., How all began: the Emergence of Life

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.
30.10. Seminar: 13; Ziya
6.11. Seminar: 6; Robert
13.11. Seminar: 8; Niko
20.11. Seminar: 10; Theresa

27.11. Modeling of Reaction-Diffusion Systems with Comsol (Comsol file)

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: 1a,b Expression cascade; Iris

4.12. Gene regulation and Stochastic Genes (1)

Regulation circuitry of protein expression.

11.12. Bacterial Chemotaxis (1,2)

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: 5 Thermophoretic Trap; Bernhard

18.12. Chemotaxis of Eukaryotes (1,2)

Chemotaxis of Dictyostelia. Outlook: Chemotaxis in Brain development.
Seminar: 15 Escalation of polymerization; Robin

8.1. Pattern formation, Hydra, Embryogenesis (1,2,3)

Biological pattern formation and morphogenesis. Activator-Inhibitor models. Structure formation in space and time. Oscillating reactions. Hydra.
Seminar: 7 Single molecule sequencing; Prishita

15.1. Neural Networks (Slides)

Basics Models and physiological Basis of Neural networks
Seminar: NN; Theresa R.

22.1. Game theory and evolution (Slides)

Description of economic processes, application in population dynamics
Seminar: 12 DNA; Laura

5.2. Oral Exams I
12.2. Oral Exams II

Exams: The exam times are set as below. They will be oral exams.
Please send your bring your filled out "Schein" to the exam. You can download the prefilled Schein here.

Exams:
Mo 5th February
13.00 xxx
13.20 xxx
...

Mo 12. February
9.00 xxx
9.20 xxx
...

pwd: evolution21