2017: Lectures and Hands-on sessions in computational molecular biophysics

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 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 in room number 3.103 in Mathematikon. The lectures/tutorials will take place once a week, on Wed from 4 to 5.30 pm (2 SWS), starting on April 26, 2017 (no lecture on April 19!). 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 Ms. Ana Herrera-Rodriguez and Dr. Agnieszka Obarska-Kosinska.

Schedule

26.04	L	Molecular Dynamics (MD), Introduction	FG
3.05	P	MD
10.05	L	MD	FG
17.05	P	MD
24.05	L	MD	FG
31.05	P	MD
7.06	L	MD	FG
14.06	P	MD
21.06	L	Brownian Dynamics (BD)	RW
28.06	P	BD
5.07	L	BD	RW
12.07	P	BD
19.07	L+P	DNA	FG
26.07	P	Questions and answers

L: lecture
P: practical
FG: Frauke Gräter
RW: Rebecca Wade.

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