Arbeitsgruppe Prof. Urbassek

Biophysik 6 WS13/14 - Molekulares Modellieren


Übung am 27.11.2013 und 04.12.2013 im CIP Raum (46-306).

CIP-Account erforderlich!

Klausur: 29.01.2014


Vorlesung 1: Einführung

Vorlesung 2: Force fields und Wasser

Übung 1: Einführung in Linux und VMD

Übung 2: MD-Simulation



  • Martin B.:
    D. Collin, F. Ritort, C. Jarzynski, S. B. Smith, I. Tinoco and C. Bustamante: Verification of the Crooks fluctuation theorem and recovery of {RNA} folding free energies. Nature 437 (2005) 231.
  • Michel B.:
    Utkur Mirsaidov, Jeffrey Comer, Valentin Dimitrov, Aleksei Aksimentiev and Gregory Timp: Slowing the translocation of double-stranded DNA using a nanopore smaller than the double helix. Nanotechnology 21 (2010) 395501.
  • Miriam E.:
    Arun K. Nair, Alfonso Gautieri, Shu-Wei Chang & Markus J. Buehler: Molecular mechanics of mineralized collagen fibrils in bone. Nature Communications 4 (2013) 1724.
    HTML, PDF   further information
  • Julian H.:
    Patrick Varilly and David Chandler: Water Evaporation: A Transition Path Sampling Study. J Phys Chem B 117 (2013) 1419.
  • Tobias G.:
    Bert L. de Groot and Helmut Grubmüller: Water Permeation Across Biological Membranes: Mechhanism and Dynamics of Aquaporin-1 and GlpF. Science 294 (2001) 2353-2357.
  • Jan-Hendrik B.:
    N. Galamba: On the Effects of Temperature, Pressure, and Dissolved Salts on the Hydrogen-Bond Network of Water. J Phys Chem B 117 (2013) 1649.
  • Christian S.:
    Valerie Daggett: Protein Folding-Simulation. Chem Rev 106 (2006) 1898.


  • Anne G.:
    Marieke Schor, Jocelyne Vreede, Peter G. Bolhuis: Elucidating the Locking Mechanism of Peptides onto Growing Amyloid Fibrils through Transition Path Sampling. Biophysical Journal, Volume 103 , (2012) Pages 1296-1304.
  • Merten G.:
    Ran Friedman, Riccardo Pellarin and Amedeo Caflisch: Amyloid Aggregation on Lipid Bilayers and Its Impact on Membrane Permeability. Journal of Molecular Biology 387 (2009) 407-415.
    HTML, PDF    Videos
  • Kai K.:
    Peter L. Freddolino and Klaus Schulten: Common Structural Transitions in Explicit-Solvent Simulations of Villin Headpiece Folding. Biophysical Journal 97 2009 2338-2347.
    HTML, PDF, Videos
  • Martin K.:
    Nutt and Meuwly: CO migration in native and mutant myoglobin: Atomistic simulations for the understanding of protein, PNAS 101 (2004) 5998.
  • Johannes G.:
    Hornak, V.; Okur, A., Rizzo, R. and Simmerling, C.: HIV-1 protease flaps spontaneously open and reclose in molecular dynamics simulations, Proc. Nat. Acad. Sci. USA, 103:915-920 (2006).
  • Mona K. F.:
    G.  Zhao et al.: Mature HIV-1 capsid structure by cryo-electron microscopy and all-atom molecular dynamics, Nature 497 (2013) 643.
    HTML, PDF   Video1, Video2
  • Daniel M.:
    N. Galamba: Water's Structure around Hydrophobic Solutes and the Iceberg Model, J Phys Chem B 117 (2013) 2153.
  • Christina M.:
    Peter L. Freddolino, Anton S. Arkhipov, Steven B. Larson, Alexander McPherson, Klaus Schulten, Molecular Dynamics Simulations of the Complete Satellite Tobacco Mosaic Virus, Structure, Volume 14, Issue 3, March 2006, Pages 437-449.
    HTML, PDF   further information


Literatur zur Vorlesung:

  • A. R. Leach. Molecular modelling - principles and applications (Pearson Education Ltd., Harlow, 2001), 2. Aufl. Contains also applications on "biological systems".
  • F. Jensen: Introduction to Computational Chemistry (Wiley 2007). Focus on methods in computational chemistry. Good introductory book if you want to focus on chemistry applications
  • D. Frenkel und B. Smit. Understanding molecular simulation (Academic, San Diego, 2002), 2. Aufl. Fairly recent book. Very good background and theory on MD, MC and Stat Mech. Applications are mainly on molecular systems
  • W. Demtröder. Moleküphysik (Oldenbourg, München, 2003). For the physics of small molecules.
  • M.P. Allen and Tildesley, "Computer Simulation of Liquids", Oxford Science Publishers. (mainly MD) Excellent book on Molecular Dynamics Simulation. Explains well the relevant Statistical Mechanics. A must if you will be doing MD.
  • C. J. Cramer: Essentials of Computational Chemistry - Theories and Models (Wiley, Chichester, 2004) 2nd edition. With a focus on chemistry issues.
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