WiSe 2013/2014: Theoretical and Computational Biophysics

Lecture series and hands-on computer tutorial (Vorlesung mit Übung)

Course Description

Lecturer: Bert de Groot, Helmut Grubmüller and Jochen Hub

This combined lecture and hands-on computer tutorial focuses on the basics of computational biophysics and deals with questions like "How can the particle dynamics of thousands of atoms be described precisely?" or "How does a sequence alignment algorithm function?"

The aim of the lecture is to develop a physical understanding of those "nano maschines" by using modern concepts of non-equilibrium thermodynamics and computer simulations of the dynamics on an atomistic scale. Moreover, the lecture shows (by means of examples) how computers can be used in modern biophysics, e.g. to simulate the dynamics of biomolecular systems or to calculate or refine a protein structure. No cell could live without the highly specialized macromolecules. Proteins enable virtually all tasks in our bodies, e.g. photosynthesis, motion, signal transmission and information processing, transport, sensor system, and detection. The perfection of proteins had already been highly developed two billion years ago.

The following topics will be introduced and discussed: Protein structure and function, physics of protein dynamics, relevant intermolecular interactions, principles of molecular dynamics simulations, numeric integration, influence of approximations, efficient algorithms, parallel programing, methods of electrostatics, protonation balances, influence of solvents, protein structure determination (NMR, X-ray), principal component analysis, normal mode analysis, functional mechanisms in proteins, bioinformatics: sequence comparison, protein structure prediction, homology modeling, and hands-on computer simulation.

The course focuses on the basic concepts and techniques of computational biophysics, addressing questions such as "How can the dynamics, the statistical mechanics, and the quantum mechanics of biological macromolecules -- consisting of thousands of atoms -- be described sufficiently accurately to quantitatively understand their function?", or "How do sequence alignment algorithms work?". The main aim of the lecture is to acquire a fundamental physical understanding of these "nano-machines" through modern non-equilibrium thermodynamics concepts and computer simulations of their dynamics at the atomistic level. Moreover, we will demonstrate the use of computers in modern biophysics, e.g. to derive and refine protein structures from experimental data and, ultimately, to understand the function of these biological nano-machines.

Without these highly specialised macromolecules, no cell would survive. In fact, virtually all tasks in our bodies, e.g. photosynthesis, motion, signal transmission and information processing, transport, sensor system, and detection, are performed or driven by proteins, which have been optimized and perfected by evolution over the past two billion years.

Time and Place

Mondays, 16:00-17:30 Lecture Hall or PC Pool Room

The course alternates between the two rooms in the Physics Faculty: Lectures take place in a lecture hall and the hands-on computer tutorials take place in a PC-Pool room of the Physics Faculty, Friedrich-Hund-Platz 1, 37077 Göttingen.


To conduct the hands-on computer tutorial, you need access to the CIP-Pool computers at the Physics Faculty. If you do not possess such an account yet, please contact the local CIP-Pool Administrator office in room C.00.101 or write an Email to: . You need to complete an application form, get the signature of a docent and hand it over to the CIP-Pool Admin-office in advance.


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