2018: 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 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 Ms. 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

Date	L/P	Topic	Lecturer
16.10.	L	Introduction into Mechanobiology, MD	FG
23.10.	L	Monte Carlo, MD and force fields	FG
30.10.	P	MD: argon	FG
6.11.	P	MD: ubiquitin	FG
13.11.	L	MD and force probe MD	FG
20.11.	P	MD: ubiquitin	FG
27.11.	L	Calculating free energies in MD	FG
4.12.	P	force-probe MD: ubiquitin	FG
11.12.	L	Coarse-grained and multi-scale MD	FG
18.12.	L/P	finite element analysis DNA	FG	assignment
8.1.	L	Continuum electrostatics	RW
15.1.	P	Continuum electrostatics	RW
22.1.	L	BD	RW
29.1.	P	BD	RW
5.2.		Question & Answers	FG

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