The University of Konstanz is one of the nine Excellence Universities of 
the Federal Republic of Germany.

Konstanz Research School - Chemical Biology (KoRS-CB): Research and 
Graduate Training at the Interface of Chemistry and Biology.
The newly founded "Konstanz Research School - Chemical Biology" (KoRS-CB) 
is an interdisciplinary initiative of the Departments of Biology, 
Chemistry, and Computer and Information Science at the University 
of Konstanz and is supported by the German Excellence Initiative.

The main objective of KoRS-CB is to guide talented graduate students to 
scientific excellence in an area that is highly relevant for both basic 
and applied research. The research program of KoRS-CB comprises the 
research areas Synthetic Chemistry, Cellular Biochemistry, Biophysics, 
Biomedicine, and Computational Biology.

KoRS-CB will commence its training program in April 2008. Thus, KoRS-CB 
invites applications for FELLOWSHIPS FOR PH.D. STUDENTS from highly 
motivated and enthusiastic students with a keen interest in 
interdisciplinary research and an excellent degree (Master or Diploma)
in Biology, Chemistry or related areas.

The University of Konstanz is a true campus university located on spacious 
grounds within one of the most beautiful areas of Germany overlooking Lake 
Constance and close to the Alps. The University of Konstanz is one of nine 
German universities that have been awarded the status of a "University of 
Excellence" by the German Excellence Initiative and provides state-of-the-
art research facilities for interdisciplinary and cutting-edge research.

PROJECT P1: Analysis of Molecular Dynamics Simulation of Complex 
Biochemical Systems

Molecular dynamics simulations are increasingly used to analyze, explain, 
and predict very complex processes in biological systems on an atomic 
level (like protein folding and drug-receptor interactions). In these 
simulations, the movement of all atoms is calculated with a time step of 
1 to 2 fs over a total simulation time of ns to ms. In this way, an 
ensemble of 106 to 109 conformations of the system composed out of up to 
100000 atoms and more is generated, which describe, on the one hand, the 
thermal fluctuations of the atoms around stable conformations of the 
biomacromolecules, and, on the other hand, the more interesting global 
movements of larger domains needed for the biological function. But due 
to the huge amount of data, it is very difficult to extract these latter, 
essential movements. Therefore, data-mining techniques, like clustering, 
will be adapted to automatically group and make sense of the information 
in a simulation trajectory. It is important that the criteria for such a 
clustering will be determined with respect to the data at hand. In the 
beginning of the investigation, it is not clear, which part of a specific 
molecular systems plays the dominate role leading to the conformational 
change. Even large movements of protein domains can be initialized by 
rotations of single amino-acid side chains. A hierarchical approach using 
different abstraction levels is anticipated for finding the global changes 
but then also to look into the local changes on the paths leading to the 
global ones. After this analysis, the different levels will be visualized 
for better interpretability by the investigator. Here, new interactive 
techniques are needed to highlight the extracted dynamical processes.

For details on the application procedure and further information on the 
research and training program of KoRS-CB, the participating Departments 
and the University of Konstanz, please visit the KoRS-CB homepage at 
http://www.chembiol.uni-konstanz.de or contact Ms Ilonka Muench, - 
e-mail: ChemBiol|,|uni-konstanz.de Konstanz Research School Chemical 
Biology, University of Konstanz, 78457 Konstanz, Germany.

Please send your application to the office of the Konstanz Research 
School Chemical Biology in single file via Email to: 
chembiol|,|uni-konstanz.de until October 1, 2008.