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Biophysics of Systems (Master) – Übersicht

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Informationen zur Vorlesung

Zeit und Ort

Friday 8.45 - 10.00 and 12.15-14.00
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 yields 4 credit points). The lecture is for Master students, background on Cellular Biophysics, Molecular Biophysics and Theoretical Biophysics is helpful and recommended. Lecture is within the Biophysics Program of the Physics Master

21.10. Introduction to Biophysics of Systems

From Evolution to (Synthetic) Biology. Introduction to the topic and the lecture.
Presentation of Seminar Topics - decisions on Seminar Slots. Seminar papers als .ZIP, pass see below right.

28.10. 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.

04.11. 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, Tamara Ehm + Philipp Schwintek

11.11. 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: #5 Replication in a thermal trap, Merlin Klotz + Pauline Kolbeck

18.11. 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: Johannes Hochholzer + Isabelle Stüwe

25.11. Chemotaxis of Eukaryotes

Chemotaxis of Dictyostelia. Outlook: Chemotaxis in Brain development.
Seminar: #13 Lattice light sheet microscopy: Stefanie Pritzl + Eduard Unterauer

02.12. Embryogenesis and Pattern formation (Eukaryote Chemotaxis, Neural Growth Cones, Embrygenesis, Pattern formation, Hydra)

Biological pattern formation and morphogenesis. Activator-Inhibitor models. Structure formation in space and time. Oscillating reactions. Hydra. Embyrogenesis.
Seminar: #3 Probing fitness landscapes of evolution: Jonas Neipel + Fatih Turan

09.12. High Throughput Methods and Synthetic Biology (Methods)

Experimental foundations, overview over different methods
Seminar: #7 Single molecule sequencing: Lea Wassermann + Sophia Gruber

16.12. 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: #4 Designed enzyme networks in a flow reactor: Sebastian Trost + Julian Stamp

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

Basics, Lac Operon, Boolean networks, Intrinsic and extrinsic noise
Seminar: #1 Reconstituted Cells: Anna Weiß + Simone Ezendam

13.01. Neural Networks (Slides)

Basics Models and physiological Basis of Neural networks
Seminar: #12 DNA Origami on membranes: Niko Bachsoliani + Keti Parlagashvili

20.01. Game theory and evolution (Slides)

Description of economic processes, application in population dynamics
Seminar: #28 Entropic DNA machines: David Lappe + David Böhringer

27.01. 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: #8 Measurement of binding: Microscale thermophoresis: Konstantin Ditzel

03.02. and 10.02. Oral exams (15 minutes each)
Oral exams are in the Labs of Prof. Braun (NU115, below machine shop)

Reminder: Time Slots of the exams as PDF
Please bring your filled out "Scheine" 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 Mandy Häusler is around.

pwd: biophysics

Verantwortlich für den Inhalt: Dieter Braun