Term paper summer semester 22: When Physics meets Biology

Docents:

• PD Dr. Steffen Wolf
• Prof. Dr. Gerhard Stock
• Prof. Dr. Jens Timmer

Time and Location: Monday 3:30 p.m., Seminar room, 10. floor

Start: May 23. 2022

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
  
  
• Principles of Maximum Entropy and Maximum Caliber
  • Literature:
    • Ghosh et al., Am. J. Phys. 74, 123 (2006)
  • Supervisor: Stock
  
  
• Enhanced Sampling of Biomolecluar Dynamics: Umbrella Sampling
  • Literature:
    • J. Kaestner WIREs Comput Mol Sci 1, 932-942 (2011)
  • Supervisor: Wolf
  
  
• Protein Folding Models
  • Literature:
    • R. Zwanzig et al. PNAS 89, 20 (1992)
    • D.J. Bicout and A. Szabo Prot. Science 9, 452 (2000)
  • Supervisor: Wolf
  
  
• Transition State Theory
  • Literature:
    • H.A. Kramers. Physica 7, 284 (1940)
  • Supervisor: Wolf
  
  
• Network-Motifs
  • Topic 1:
    • 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
  • Topic 2:
    • L. Goentoro et al. The incoherent feedforward loop can provide fold-change detection in gene regulation. Molecular Cell 36: 894-899, 2009
    • M. Adler, U. Alon. Fold-change detection in biological systems. Current Opinion in Systems Biology 8:81-89, 2018
  • 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
  
  
• Pattern formation
  • Topic 1:
    • A. Turing. The Chemical Basis of Morphogenesis. Philosophical Transactions of the Royal Society of London B. 237 (641). pp. 37-72
  • Topic 2:
    • A. Gierer, H. Meinhardt. A Theory of Biological Pattern Formation. Kybernetik 12, 30-39 (1972)
  • Supervisor: Timmer
  
  

Programme:

• May 23:

• May 30:

• June 13:

• June 20:

• June 27:

• July 4:

• July 11:

• July 18:

• July 25: