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Biophysics of Systems (Master) – Übersicht

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Informationen zur Vorlesung

Zeit und Ort

Monday 14.00 - 16.15 and 16.15 - 17.00
N020 (kleiner Physikalische Hörsaal)

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

15.10. Introduction to Biophysics of Systems

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

22.10. How all began: the Emergence of Life (Part 1)
(Lecture PDF, Talk replicative symmetry breaking, Talk Karin Öberg, Libreoffice files)

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.

29.10. How all began: the Emergence of Life (Part 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: #2 Spiegelman, Tyranny of the shortest (Samuel Stubhan, Slides)

5.11. Bacterial Chemotaxis
(Slides, Labview ODE, As Windows Install)

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: #3 Fitness Landscapes (no talk)

12.11. Modeling of chemical Networks
(+Matlab introduction) [Slides and Code]

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: #10 RNA world (Tapan Joshi; Monique Honsa, Slides)

19.11. Chemotaxis of Eukaryotes (Slides and Mathlab Code)

Chemotaxis of Dictyostelia. Outlook: Chemotaxis in Brain development.
Seminar: #5 Replication in a thermal trap (Jongseo Kim; Simon Langnickel, Slides)

26.11. Embryogenesis and Pattern formation
(Embrygenesis, Pattern formation, Hydra)

Biological pattern formation and morphogenesis. Activator-Inhibitor models. Structure formation in space and time. Oscillating reactions. Hydra. Embyrogenesis.
Seminar: #13 Lattice light sheet microscopy (Francesco Ippolito, Mario Gaimann)

3.12. High Throughput Methods and Synthetic Biology
(Methods) (Synthetic Biology)

Experimental foundations, overview over different methods
Seminar: #7 Single molecule sequencing (Maximilian Weingart; Nina Beier, Slides)

10.12. Modeling of Reaction-Diffusion Systems /
(+Comsol introduction) [Comsol Models]

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 Reconstituted Cells (Zahra Mohaveri; Maria Ponetsmüller, Slides )

17.12. Gene Regulation and stochastic effects in regulatory networks.
Regulation using RNA: Splicing, RNA folding, Interference RNA (Expression I)(Expression II) (Expression III) (RNAinterference) (Riboswitches)

Basics, Lac Operon, Boolean networks, Intrinsic and extrinsic noise
Seminar: #11 Stochasticity of single cellmetabolism (Cristina Leonardo; Hang Li)

7.01. Neural Networks (Slides)

Basics Models and physiological Basis of Neural networks
Seminar: #20 Next generation sequencing (Flavio Auer; Erik Kubasek)

14.01. Game theory and evolution (Slides)

Description of economic processes, application in population dynamics
Seminar: #8 Physarium as model organizsm for flow networks (Roland Szakacs; Christoph Pauer, Talk file)

21.01. 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: #6 Cell-free systems on a chip (Diminik Sailer; Michael Redl)

28.01. and 4.02. Oral exams (15 minutes each)
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, at best in the Morning when our Lab assistant Mandy Häusler is around.

pwd: biophysics

Verantwortlich für den Inhalt: Dieter Braun