Term paper winter semester 18/19: When Physics meets Biology

Professors:

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

Time and Location: Wednesday, 16:15, Seminarroom, 10. floor

Start: Nov. 21, 2016

The text to be written should be four pages

Possible topics:

• Nonequilibrium Statistical Mechanics: The Langevin Equation
  • Literature:
    • R. Zwanzig. Oxford University Press (2001)
  • Supervisor: Stock
  
  
• Markov Models of Protein Dynamics,
  • Literature:
    • J.-H. Prinz et al. J. Chem. Phys. 134, 174105 (2011)
  • Supervisor: Stock
  
  
• Protein Folding Models
  • Literature:
    • R. Zwanzig et al. PNAS 89, 20 (1992)
    • D.J. Bicout and A. Szabo Prot. Science 9, 452 (2000)
  • Supervisor: Stock
  
  
• Transition State Theory
  • Literature:
    • H.A. Kramers. Physica 7, 284 (1940)
  • Supervisor: Stock
  
  
• Two-Dimensional Spectroscopy of Biomolecular Dynamics
  • Literature:
    • Woutersen and Hamm, J. Phys. Condens. Matter 14, R1035 (2002)
  • Supervisor: Stock
  
  
• Principles of Maximum Entropy and Maximum Caliber
  • Literature:
    • Ghosh et al., Am. J. Phys. 74, 123 (2006)
  • Supervisor: Stock
  
  
• Network-Motifs
  • Literature:
    • R. Milo et al. Network Motifs: Simple Building Blocks of Complex Networks. Science 298:824-827 (2002) and Supplement
    • S. Shen-Orr et al. 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:

• 21. 11. 2018
  Leonhard Haegele: The Langevin Equation

• 28. 11. 2018
  Georg Diez: Markov models

• 05. 12. 2018
  David Steinbrecht: Pattern Formation

• 12. 12. 2018
  Moritz Spreter: Protein folding models

• 19. 12. 2018
  Nikos Molochidis: Action potentials

• 9. 1. 2019
  Oscar Henriques: Network Motifs

• 16. 1. 2019
  Benjamin Winkelmann: Transition State Theory

• 23. 1. 2019
  Yasaman Heshmatzadeh: Signaling Cascades

• 30. 1. 2019
  Xu Yualin: Principles of Maximum Entropy and Maximum Caliber