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.

14.10. No Lecture in the first week (conference in the US - sorry)

21.10. Introduction to Biophysics of Systems

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

28.10. How it all began: overview over the Origin of Life 1

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.

4.11. Origin of Life 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.

11.11. Origin of Life 3

18.11., Origin of Life 4

25.11. Modeling of Reaction-Diffusion Systems with Comsol (Slides 1,2,3)

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: 7 Real-Time DNA Sequencing from Single Polymerase Molecules, Lena E.

2.12. Gene regulation and Stochastic Genes

Regulation circuitry of protein expression.
Seminar: Heat flows enrich prebiotic building blocks and enhance their reactivity, Tianyi C. (ausgefallen)

9.12. 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 within receptor fields.
Seminar:

16.12. Chemotaxis of Eukaryotes

Chemotaxis of Dictyostelia. Outlook: Chemotaxis in Brain development.
Seminar: Entropic RNA machines, Gkionis A.

13.1. Pattern formation, Hydra, Embryogenesis

Biological pattern formation and morphogenesis. Activator-Inhibitor models. Structure formation in space and time. Oscillating reactions. Hydra.
Seminar: 20a_next_generation_sequencing, Shanglai J.

20.1. Neural Networks

Basics Models and physiological Basis of Neural networks
Seminar: Topic 13, Stefan S.

27.1. Game theory and evolution

Description of economic processes, application in population dynamics. 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: Topic 12b, Charlie P.

3.2. Oral Exams

Exams: The exam times are set in the Lecture
Please send your bring your filled out "Schein" to the exam for Masters according to old rules.

Exams:
Mo 3th February
13.00 xxx
13.20 xxx
...
 

pwd: evolution21