Studenten Seminar: Physik in der Biologie

Dozenten:

• Prof. Dr. J. Timmer
• mit freundlicher Unterstützung von Dr. Ch. Fleck und Dr. S. Reinker

Zeit und Ort: Di. 17-19, SR I

Beginn: 25.4.05

Vorbesprechung: Di. 4.4.05, 17 Uhr ct, SR I

Programm:

• 25.4.06
  
  • Vortragender: Sven Goedecke
  • Thema: Musterbildung in Reaktions-Diffusions Gleichungen
  • Literatur:
    • J. D. Murray, How the leopard gets its spots, Scientific American, March 1988, p. 80.
    • J. D. Murray, Mathematical Biology (Springer-Verlag, Berlin,1989). Kapitel 14
    • Gierer, A. and H. Meinhardt (1972), A theory of biological pattern formation. Kybernetik 12, 30-39.
    • Anwendung je nach Geschmack (Fliegenembryo, Tierfelle, chemische Reaktionen, Haarmuster)
  • Betreuer: Reinker

• 2.5.06
  
  • Vortragender: Peter Baumann
  • Thema: Räumliche Systeme, gebrochene Symmetrien und Musterbildung: Complexe Ginzburg-Landau Gleichung
  • Literatur:
    • Pattern formation outside of equilibrium. Cross and Hohenberg, Rev. Mod. Phys. 65,3 1993
    • The world of complex Ginzburg-Landau equation. Aranson and Kramer, Rev. Mod. Phys. 74,1 2002
    • Kap. 5 Murray "Mathematical Biology II", Springer Verlag 2004
    • One Hundred Years of Nonequilibrium Patterns. Hohenberg, Physikalische Blätter 55, 1999
    • "Spatially distributed systems, broken symmetries, pattern formation" Kap.5&6 aus G. Nicolis "Introduction to Nonlinear Systems", Cambridge University Press
  • Betreuer: Fleck

• 9.5.06
  
  • Vortragender: Simon Amrein
  • Thema: Stochastische Prozesse: Theoretische Grundlagen
  • Literatur:
    • Gillespie, D. T. "Exact Stochastic Simulation of Coupled Chemical Reactions." J. Phys. Chem. 81 (1977): 2341-61.
    • O. Wolkenhauer, M. Ullah, W. Kolch, K.H. Cho Modeling and simulation of intracellular dynamics: choosing an appropriate framework IEEE Trans Nanobioscience. 3(3):200, 2004.
  • Betreuer: Reinker

• 16.5.06
  
  • Vortragende: Kathrin Henschel
  • Thema: Stochastische Prozesse: Biologische Anwendungen
  • Literatur:
    • Arkin, A., J. Ross, and H. H. McAdams. "Stochastic Kinetic Analysis of Developmental Pathway Bifurcation in Phage lambda-infected Escherichia Coli Cells." Genetics 149 (1998): 1633-48.
    • McAdams, H. H., and A. Arkin. "Stochastic Mechanisms in Gene Expression." Proc. Natl. Acad. Sci. USA 94 (1997): 814-9.
    • I Golding, J Paulsson, SM Zawilski, EC Cox Real-time kinetics of gene activity in individual bacteria. Cell. 2005 Dec 16;123(6):1025-36.
  • Betreuer: Reinker

• 23.5.06
  
  • Vortragender: Janosch Deeg
  • Thema: Dynamische Strukturbildung in Zellen
  • Literatur:
    • A Mechanism for Polar Protein Localization in Bacteria. M. Howard J. Mol. Biol. 335, 655 2004
    • Pattern Formation inside Bacteria: Fluctuation due to the Low Copy Number of Proteins. M. Howard and A. Rutenberg, Phys. Rev. Lett. 90,12 128102 2003
    • A stochastic model of Min oscillations in Escherichia coli and Min protein segregation during cell division. F. Tostevin and M. Howard, Phys. Biol. 3, 1 2006
    • M. Howard, A.D. Rutenberg, S. de Vet. Dynamic Compartmentalization of Bacteria: Accurate division in E. Coli. Phys. Rev. Lett. 87, 278102, 2001
    • D.M. Raskin, P.A.J. de Boer. Rapid pole-to-pole oscillation of a protein required for directing division to the middle of Escherichia coli. Proc. Natl. Acad. Sci. 96, 4971-4976, 1999
    • Rahul V. Kulkarni et al. Pattern Formation within Escherichia coli: Diffusion, Membrane Attachment, and Self-Interaction of MinD Molecules Phys. Rev. Lett. 93, 228103, 2004
  • Betreuer: Fleck

• 30.5.06
  
  • Vortragende: Tanja Schmitt
  • Thema: Membranphysik
  • Literatur:
    • Statistical Mechanics of Membranes and Surfaces. Edited by D. Nelson, T. Piran and S. Weinberg, World Scientific1989
    • Configurations of fluid membranes and vesicles. U. Seifert, Adv. Phys., 46,1 13 1997
    • Structure and Dynamics of Membranes. Elsevier Science, Amsterdam, 1994.
    • Fluid vesicles. U. Seifert, Lecture Notes: 'Physics meets Biology. From Soft Matter to Cell Biology', Forschungszentrum Jülich 2004
    • Mikromechanik der Zelle. E. Sackmann, Physik Journal, 3,2 2004
    • Cell and molecular mechanics of biological materials. G. Bao and S. Suresh, Nature Materials, 2 2003
  • Betreuer: Fleck

• 13.6.06
  
  • Vortragender: Tim Meyer
  • Thema: Motorproteine
  • Literatur:
    • Biologische Motoren. P. Lenz, Physik Journal 3,6 2004
    • Forces and Motion Generation of Molecular Motors: A Generic Description. F. Jülicher
    • Modeling molecular motors. F. Jülicher et al. Rev. Mod. Phys. 69, 1269 1997
    • Kap. 18 aus Mathematical Physiology. J. Keener and J. Sneyd, Springer Verlag
    • The Turn of the Screw: Minireview The Bacterial Flagellar Motor. Cell, Vol. 93, 17 1998,
    • The bacterial flagellum and flagellar motor: structure, assembly and function. C. Jones and S. Aizawa, Adv Microb Physiol. 32:109 1991
    • The bacterial flagellar motor: structure and function of a complex molecular machine. S. Kojima and D. Blair, Int Rev Cytol. 233: 93 2004
    • The Rotary Motor of Bacterial Flagella. Ann. Rev. Biochem. Vol. 72:19 2003
  • Betreuer: Fleck

• 20.6.06
  
  • Vortragende: Linda Spindeler
  • Thema: Modellierung der cerebralen CO2-Reaktivität
  • Literatur:
    • M.J. Poulin, P.J. Liang and P.A. Robbins. Dynamics of the cerebral blood flow response to step changes in end-tidal PCO2 and PO2 in humans, J Appl Physiol 81, 1084-1095, 1996
    • M.J. Poulin, P.J. Liang, P.A. Robbins. Fast and slow components of cerebral blood flow response to step decreases in end-tidal PCO2 in humans. J Appl Physiol 85, 388-397, 1998
  • Betreuer: Timmer

• 27.6.06
  
  • Vortragender: Simon Thiele
  • Thema: Mechanik der Geisseldrehung
  • Literatur:
    • Life at Low Reynolds Number. E. Purcell, American Journal of Physics 45, 3 1977
    • The efficiency of propulsion by a rotating flagellum. E. Purcell, PNAS 94, 11307 1997
    • Flagellar Hydrodynamics: The John von Neumann Lecture, 1975. J. Lighthill
    • The role of hydrodynamic interaction in the locomotion of microorganisms. M. Ramia et al. Biophys J. 65(2): 755 1993
    • Motile behavior of bacteria. H. Berg, Physics Today, 53, 24 2000
    • Hydrodynamics of flagellar propulsion - helical waves. J. Higdon, J. Fluid Mech. 94, 331 1979
    • Hydrodynamic interactions between rotating helices. M. Kim and T. Powers. Phys. Rev. E 69, 061910 2004
    • Swimming in circles: Motion of Bacteria near Solid Boundaries. E. Lauga et al. Biophys. J. 90: 400 2006
  • Betreuer: Fleck

• 4.7.06
  
  • Vortragender: Raphael Engesser
  • Thema: Synchronisation schwach gekoppelter Oszillatoren I: Theoretische Grundlagen
  • Literatur:
    • Strogatz, S. H., and I. Stewart. 1993. Coupled oscillators and biological synchronization. Scientific American 269 (6):102-09.
    • A.T. Winfree, The Geometry of Biological Time, 2nd ed., Springer, New York, 2001. Kapitel 3, 4
    • A. Pikovsky, M. Rosenblum, J. Kurths. Synchronization. A universal concept in nonlinear sciences. Cambridge University Press 2001. Kapitel 2, 4.
    • E.M. Izhikevich, Y. Kuramoto Weakly coupled oscillators. Encyclopedia of Mathematical Physics, Elsevier 2006
  • Betreuer: Reinker

• 11.7.06
  
  • Vortragender: David Feess
  • Thema: Synchronisation schwach gekoppelter Oszillatoren II: Biologische Anwendungen
  • Literatur:
    • A. Pikovsky, M. Rosenblum, J. Kurths. Synchronization. A universal concept in nonlinear sciences. Cambridge University Press 2001.
    • A.T. Winfree, The Geometry of Biological Time, 2nd ed., Springer, New York, 2001. Jeweils verschiedene Beispiele
    • L. Glass. Synchronization and rhythmic processes in physiology. Nature, 410, 277-284 (2001) (Insight review article)
  • Betreuer: Reinker

• 18.7.06
  
  • Vortragender: Stefan Waselikowski & Johannes Asal
  • Thema: Physik des Innenohrs
  • Literatur:
    • Kap. 23 aus Mathematical Physiology. J. Keener and J. Sneyd, Springer Verlag
    • Mechanical amplification of stimuli by hair cells. A. Hudspeth, Curr. Op. Neurobiol. 7, 480 1997
    • Comparison of a hair bundle's spontaneous oscillations with its response to mechanical stimulation reveals the underlying active process. P. Martin et al., PNAS 98, 25 14380 2001
    • Active hair-bundle motility harness noise to operate near an optimum of mechanosensitivity. B. Nadrowski et al., PNAS 101,33 12195 2004
  • Betreuer: Fleck

• 25.7.06
  
  • Vortragender: Florian Posdziech
  • Thema: Herzdynamik
  • Literatur:
    • J. Keener, J. Sneyd Mathematical Physiology, Springer Verlag. Kapitel 11, 14
    • Noble D. Modelling the heart: from genes to cells to the whole organ. Science 2002; 295: 1678-1682.
    • M.R. Guevara, A. Shrier, L. Glass. Phase-locked rhythms in periodically stimulated heart cell aggregates. American Journal of Physiology 254 (Heart Circ. Physiol. 23), H1-H10 (1988).
  • Betreuer: Reinker