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, game theory and econophysics of money. The lecture will include a short introduction in modeling of chemical networks with MatLab and reaction-diffusion systems with Comsol. It is a 3 hour lecture, 1 hour seminar, 6 Credit Points, Only the lecture results in 4 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. Introduction to Biophysics of Systems (Slides intro, Slides Seminar)

From Evolution to (Synthetic) Biology. Introduction to the topic and the lecture.
Presentation of Seminar Topics - decisions on Seminar Slots. Seminar papers are found here.

21.10. How all began: the Emergence of Life (IntroTalk)

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., 4.11., 11.11, 18.11., How all began: the Emergence of Life (Evolution history, Cooperating Ligation, Molecules in Space, Habitable zones)

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.
28.10.: Seminar: #3 Fitness Landscapes, Antonia Hager+Yicui Kang
4.11..: Seminar: #2 Arina Kuznetsova + Amin Akermi
11.11.: Seminar: #12 DNA Origami Jonas Fischer + Philipp Steen (Slides)
18.11.: Seminar: #14 Susanne Reinhardt + Anna Baptist (Slides Artificial Cells)

25.11. Bacterial Chemotaxis (Slides, Talk Cremer)

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: #28 DNA machines: Lucas Fochler + Benjamin Kahlert (Slides) and #11 Stochastic Metabolism: Carlos Christian Sustay Martinez + Leopold Brünnig

2.12. Chemotaxis of Eukaryotes (Slides, Neural growth cones)

Chemotaxis of Dictyostelia. Outlook: Chemotaxis in Brain development.
Seminar: #9 Single Molecular Protein Function Andreas Schmid

9.12. Hydra (Slides), Embryogenesis (Slides), Pattern formation (Slides), Gene regulation (Slides), Stochastic Genes (Slides)

Biological pattern formation and morphogenesis. Activator-Inhibitor models. Structure formation in space and time. Oscillating reactions. Hydra. Embyrogenesis.
Seminar: #4 Leonardo Demarchi + Michael Ryczkowski

16.12. Modeling of Reaction-Diffusion Systems with 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: #1 Cell Free Georg Ladurner + Vinzenz Velten (Talk as ZIP-File)

23.12. Neural Networks (Slides)

Basics Models and physiological Basis of Neural networks
Seminar: #20 Illumina Sequencing Tassilo von Trotha + Joachim Rössner

13.01. Game theory and evolution (Slides)

Description of economic processes, application in population dynamics
Seminar: #7 Single Molecule sequencing Maximilian Voggenthaler + Sabina Orazov

20.01. Physically motivated models of monetary exchange (Feynman-Bookkeeping, Mirror Money (In)Stability)

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: #6 Cell free on a chip Felix Brandner + Max Kreft

The exams take place on Febr. 27 and March 6. If you are not scheduled yet for the examinations, please contact our lab assistant rueter-stimpfle@physik.lmu.de. There are still slots on March 6 from 5pm on.

Oral exams are in the Labs of Prof. Braun (NU115, below machine shop)

Please bring your filled out "Schein" to the exam - I will fill them out after the two days of exams. They can be picked up in our Lab.

27.02. Examinations

06.03. Examinations

pwd: biophysics