Ankündigung

Übung am 06.01.2016 und 13.01.2016 im CIP Raum (46-306): RHRK-Account erforderlich!

Klausur: 10.2.2016, 10 Uhr 46-576

Nachklausur: 13.4.2016, 10 Uhr, 46-208

Vorlesung

Inhalt

Lernziele

Vorlesung 1: Einführung

Vorlesung 2: Force fields und Wasser

Vorträge:

27.01.2016

• Florian M.:
  Vincent A. Voelz, Gregory R. Bowman, Kyle Beauchamp and Vijay S. Pande. Molecular Simulation of ab Initio Protein Folding for a Millisecond Folder NTL9(1−39). J. Am. Chem. Soc. 132 (2010) 1526–1528.
  HTML, PDF
• Jan Christoph S.:
  Yang Li, Haipeng Gong. Theoretical and simulation studies on voltage-gated sodium channels. Protein Cell 6 (2015) 413–422.
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• Tatjana S.:
  Cherezov et al.: High-Resolution Crystal Structure of an Engineered Human {beta}2-Adrenergic G Protein–Coupled Receptor, Science 318 (2007) 1258.
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  AND
  GPCR Engineering Yields High-Resolution Structural Insights into {beta}2-Adrenergic Receptor Function, Science 318 (2007) 1266.
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• Chariklia G.:
  Giuseppina Raffaini and Fabio Ganazzoli. Understanding the Performance of Biomaterials through Molecular Modeling: Crossing the Bridge between their Intrinsic Properties and the Surface Adsorption of Proteins. Macromol Biosc. 7 (2007) 552.
  HTML, PDF
• Pariyanka A.:
  Murail, S. and Howard, R. J. and Broemstrup, T. and Bertaccini, E. J. and Harris, R. A. and Trudell, J. R. and Lindahl, E. Molecular Mechanism for the Dual Alcohol Modulation of Cys-loop Receptors. PLOS Comput. Biol. 8 (2012) e1002710.
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03.02.2016

• Mirko H.:
  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
• Catharina K.:
  Mareike Zink and Helmut Grubmüller. Mechanical Properties of the Icosahedral Shell of Southern Bean Mosaic Virus: A Molecular Dynamics Study. Biophys. J. 96 (2009) 1350.
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• Fabian G.:
  Bert L. de Groot, Andreas Engel, Helmut Grubmüller: A  refined structure of human aquaporin-1. FEBS Lett.504  (2001) 206.
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• Larissa H.:
  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.
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• Katharina 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  additional information
• Sara E.:
  T. Lemaire et al. Water in hydroxyapatite nanopores: Possible implications for interstitial bone fluid flow. Journal of Biomechanics 48 (2015) 3066–3071.
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• Christopher C.:
  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

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.