Lectures and Hands-on sessions in Computational 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 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.

Lectures:

Introduction

Examples for forces in biology: bone and gravity; birds and magnetic fields; muscle and motors; ears and sound waves

Structure & dynamics of biomolecules (proteins, RNA and DNA)

Mechanics of biomolecules (polymer theories, rate theories, experiments)

Atomistic scale:

Molecular Dynamics I – approximations and force fields;

Molecular Dynamics II – integration schemes;

Molecular Dynamics III – boundaries, electrostatics, ensembles;

Molecular Dynamics IV – probing mechanics;

Monte Carlo

Mesoscopic scale:

Coarse-graining, Go models, Langevin and Brownian Dynamics

continuum approximations

Macroscopic scale:

computational mechanics, finite element methods, fracture theories;

Current challenges: bridging scales, whole virus/cell simulations

Tutorials:

MD: phase transition of argon

MD: structure and dynamics of the protein ubiquitin

MD: mechanics of ubiquitin

Brownian Dynamics

finite-element analysis of DNA mechanics

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