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2015: Lectures and Hands-on sessions in computational molecular biophysics

Date
14. October 2015
Categories

You find the lecture slides and the material for practicals here (restricted access).

Computational Molecular Biophysics: Schedule

Date L/P Topic Lecturer
14.10. L Introduction into Mechanobiology, MD FG
21.10. P MD: Argon FG
28.10. L Monte Carlo, MD and force fields FG
4.11. P MD: ubiquitin FG
11.11. L MD and force probe MD FG
18.11. L Calculating free energies in MD FG
25.11. L MD with combined quantum/classical mechanics FG
2.12. L Coarse graining, multi-scale challenges FG
9.12. P MD: ubiquitin FG
16.12. P force-probe MD: ubiquitin FG
23.12.? L L/P finite element analysis FG
13.1. P BD RW
20.1. L BD RW
27.1. P BD RW
3.2. L BD RW

 

P: practical, CIP POOL

L: lecture, seminar room

Tutors during tutorials:

Katra Kolsek, Csaba Daday, Ana Herrera-Rodriguez

How can a bird sense magnetic fields, how does our ear detect sound waves, how does our bone feel gravitation? It is the physics of individual molecules that dictate these and many other processes in life.

This course introduces computational methods to study the structure, dynamics and mechanics of biomolecules at different scales. It aims at endowing the students with an understanding of the principles, the capacity and limitations of different numerical simulation techniques with an emphasis on Molecular Dynamics simulations. The course comprises alternating lectures and hands-on computer tutorials of which the latter are meant to directly demonstrate the principles of running and analyzing computer simulations of biological matter. Lectures and hands-on computer tutorials will take place alternately in the seminar room SR043 and the CIP-Pool (both Bioquant). The lectures/tutorials will take place once a week, on Wed from 4 to 5.30 pm (2 SWS), starting now on October 14, 2015. Lectures will be given by Prof. Frauke Gräter and  Prof. Rebecca Wade.

The lectures will be targeted to advanced Bachelor, Master and interested PhD students and will be complemented by hands-on computer sessions in which the students will have the opportunity to run molecular simulations supervised by Dr. Katra Kolšek, Dr. Csaba Daday and Ms. Ana Herrera-Rodriguez.

Resources:

  1. Schlick, “Molecular Modelling and Simulation”, Springer, 2010

M.P. Allen and Tildesley, “Computer Simulation of Liquids”, Oxford Science Publishers. (Great book with a focus on Molecular Dynamics simulations)

  1. Frenkel und B. Smit. “Understanding molecular simulation” Academic, San Diego, 2002, (covers MD, MC and Stat Mech)
  2. Dill and S. Bromberg, “Molecular Driving Forces”, Taylor & Francis Inc, 2010

www.gromacs.org open source molecular simulation software used in the tutorial, for both atomistic MD and coarse-grained Brownian dynamics simulations. Comes with an extensive manual, which includes the principles of MD simulations and biomolecular force fields.

http://cando-dna-origami.org/ web-based finite element software for mechanics/dynamics of DNA sculptures

Click here to go to the German home page.