WS 2018/19: Lectures and Hands-on sessions in computational molecular biophysics

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 active understanding of the principles, the capacity and limitations of different molecular simulation techniques, including Monte Carlo, Molecular Dynamics, Brownian Dynamics and multi-scale simulations 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 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 Fabian Kutzki, Dr. Fan Jin, Dr. Kashif Sadiq and Dr. Prajwal Nandekar.

Time and place:

Lectures and hands-on computer tutorials will take place in room number 3.103 in Mathematikon. The lectures/tutorials will take place once a week, on Tuesdays, 14-15.30 pm (2 SWS).

Schedule

DateL/PTopicLecturer 
17.10.LIntroduction: Proteins & Molecular DynamicsFG 
24.10.LMolecular Dynamics and force fieldsFG 
31.10.PMD: argon in a box  
7.11.LMonte Carlo methods, non-equilibrium methodsFG 
14.11.PMD: ubiquitin  
21.11.LFree energy calculationsFG 
28.11.PMD: ubiquitin continued  
5.12.LCoarse-grained and multi-scale MDFG 
12.12.PMD: ubiquitin pulling  
19.12.LContinuum electrostaticsRW 
9.1.PContinuum electrostatics  
16.1.LBrownian DynamicsRW 
23.1.PBrownian Dynamics  
30.1.L/PFinite element methods & DNAFG 
6.2. Question & Answers 

L – lecture, P – practical, FG – Frauke Gräter, RW – Rebecca Wade

 

Deadline for the home assignement is February 13th.

Resources:

  1. Schlick, “Molecular Modelling and Simulation”, Springer, 2010
  2. M.P. Allen and Tildesley, “Computer Simulation of Liquids”, Oxford Science Publishers. (Great book with a focus on Molecular Dynamics simulations)
  3. Frenkel und B. Smit. “Understanding molecular simulation” Academic, San Diego, 2002, (covers MD, MC and Stat Mech)
  4. 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

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