Arbeitsgruppe Prof. Urbassek

Biophysik 6 WS16/17 - Molekulares Modellieren


Übung am 11.01.2017 und 18.01.2017 im CIP Raum (46-306): RHRK-Account erforderlich!

Klausur: 08.02.2017


Vorlesung 1: Einführung

Vorlesung 2: Force fields und Wasser



  • Julia K.:
    G.  Zhao et al.: Mature HIV-1 capsid structure by cryo-electron microscopy and all-atom molecular dynamics, Nature 497 (2013) 643.
    HTML, PDF  Video1Video2
  • Ben W.:
    David A. Köpfer, Chen Song, Tim Gruene, George M. Sheldrick, Ulrich Zachariae and Bert L. de Groot. Ion permeation in K+ channels occurs by direct Coulomb knock-on, Science 346 (2014) 352
  • Marius R.:
    Shaw, D. E.; Maragakis, P.; Lindorff-Larsen, K.; Piana, S.; Dror, R. O.; Eastwood, M. P.; Bank, J. A.; Jumper, J. M.; Salmon, J. K.; Shan, Y.; Wriggers, W. Atomic-Level Characterization of the Structural Dynamics of Proteins. Science 2010, 330, 341–346.
  • Jonathan O.:
    H.I. Ingolfsson, M.N. Melo, F.J. van Eerden, C. Arnarez, C. Lopez, T.A. Wassenaar, X. Periole, A.H. de Vries, D.P. Tieleman, S.J. Marrink. Lipid organization of the plasma membrane, J. Am. Chem. Soc. 136, 14554-14559.
  • Marco T.:
    Po-chia Chen and Jochen S. Hub. Interpretation of solution X-ray scattering data by explicit-solvent molecular dynamics, Biophys. J., 108, 2573–2584 (2015).
    Related New and Notable comment by Robert Rambo and John Tainer: Biophys. J. 108:2421-2423 (2015)
    HTMl, PDF

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. Molekülphysik (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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