Term paper winter semester 16/17: When Physics meets Biology

Professors:

• Prof. Dr. Thomas Filk
• Prof. Dr. Gerhard Stock
• Prof. Dr. Jens Timmer

Time and Location: Tuesday, 17:15 , Seminarroom, 10. floor

Start: 8. 11. 2016

The text to be written should be four pages

Possible topics:

• Graphs:
• Literature:
• Watts, D.J., Strogatz, S.H.; Collective dynamics of `small-world' networks; Nature, Vol. 393; 4 June 1998, pp. 440-442.
• Barabasi, A.-L., Albert, R.; Emergence of Scaling in Random Networks; Science, Vol. 286, 15 October 1999, pp. 509-512.
• Farkas, I.J., Derenyi, I., Barabasi, A.-L., Vicsek, T.; Spectra of ``real-world'' graphs: Beyond the semicircle law; Physical Review E, Vol. 64 (2001), pp. 026704 1-12.
• Supervisor: Filk

• Modelling:
• Literature:
• Parisi, G.; A simple model for the immune network; Proc. Natl. Acad. Sci. USA, Vol. 97, January 1990, pp. 429-433.
• Supervisor: Filk

• Neural Networks:
• Literature:
• Oja, E.; A Simplified Neuron Model as a Principal Component Analyzer; J. Math. Biology, Vol. 15 (1982), pp. 267-273.
• Supervisor: Filk

• Nonequilibrium Statistical Mechanics: The Langevin Equation
  • Literature:
    • R. Zwanzig Oxford University Press, Chapter 1 (2001)
  • Supervisor: Stock
  
  
• Enhanced Sampling of Biomolecluar Dynamics: Umbrella Sampling
  • Literature:
    • J. Kaestner WIREs Comput Mol Sci 1, 932-942 (2011)
  • Supervisor: Stock
  
  
• Markov State Models: Hierarchical analysis of conformational dynamics in biomolecules
  • Literature:
    • F. Noe et al. J. Chem. Phys. 126, 155102 (2007)
  • Supervisor: Stock
  
  
• The Energy Landscape of Biomolecules: Protein Folding
  • Literature:
    • K. Dill. Protein Science 8, 1166 (1999)
  • Supervisor: Stock
  
  
• Maximum Caliber: Teaching the principles of statistical dynamics
  • Literature:
    • K. Ghosh et al. Am J. Phys. 74, 123 (2006).
  • Supervisor: Stock
  
  
• Network-Motifs
  • Literature:
    • R. Milo, S. Shen-Orr, S. Itzkovitz, N. Kashtan, D. Chklovskii, U. Alon. Network Motifs: Simple Building Blocks of Complex Networks. Science 298:824-827 (2002) and Supplement
    • S. Shen-Orr, R. Milo, S. Mangan, U. Alon. Network motifs in the transcriptional regulation network of Escherichia coli. Nature Genetics, 31:64-68 (2002). and Supplement
    • U. Alon. Network motifs: theory and experimental approaches. Nature Review Genetics 8:450-461, 2007
  • Supervisor: Timmer
  
  
• Signaling Cascades
  • Literature:
    • R. Heinrich, B.G. Neel, T.A. Rapoport. Mathematical models of the protein kinase signal transduction. Molecular Cell 9:957-970, 2002
  • Supervisor: Timmer
  
  
• Action potentials
  • Literature:
    • A.L. Hodgkin, A.F. Huxley. A quantitative description of membrane current and its application to conduction and excitation in nerve. J. Physiology 117:500-544, 1952
  • Supervisor: Timmer
  
  
• Pattern formation
  • Literature:
    • A. Turing. The Chemical Basis of Morphogenesis. Philosophical Transactions of the Royal Society of London B. 237 (641). pp. 37–72
    • A. Gierer, H. Meinhardt. A Theory of Biological Pattern Formation. Kybernetik 12, 30-39 (1972)
  • Supervisor: Timmer
  
  

Programme:

• 8. 11. 2016
  Max Jakob, Topic: Action potentials, ,

• 15. 11. 2016
  Simon Tamyalew, Topic: Modelling the immune system, ,

• 22. 11. 2016
  Tilman Eichhorn, Topic: Neural Networks, ,

• 29. 11. 2016
  Severin Bang, Topic: Pattern Formation, ,

• 06. 12. 2016
  Elisabeth Schula, Topic: Graphs, ,

• 13. 12. 2016
  Moritz Bitterling, Topic: Networks Motifs, ,

• 20. 12. 2016
  Franz-Georg Wieland, Topic: Markov State Models, ,

• 10. 01. 2017
  Charlotte Voigt, Topic: Energy Landscape, ,

• 17. 01. 2017
  Motaya Suzka, Topic: Signaling Cascade, ,

• 24.01.2017
  Anna Weber, Topic: Langevin equation, ,

• still one slot available