Competence Center Bioinformatics

Research

Abstracts of Research

Computer Models of DNA Chromatin

DNA is the carrier of the genetic information in the nucleus. In higher organisms DNA is complexed with proteins forming a bead-on-a-sting like structure. This structure condeses into the so called chromatin. The chromosomes are formed by chromatin.

A model of chromatin fiber will be developed that describes its spatial organization and dynamic properties. The model uses the nucleosomes and linker DNA as building blocks (size about 10 nm) to construct long fiber fragments with 500 nucleosomes (length about 1┬Ám) and more, to study also the higher order folding of the fiber. The work is based on Monte Carlo simulations that will be complemented with analytical description. The features of the models will be tested and developed against experimental data from scanning force microscopy and force spectroscopy experiments. The simulations will help to identify parameters that determine the dynamic conformation of the chromatin fiber. These are potential targets for biological factors that induce a transcriptionally active conformation of the fiber. Accordingly, predictions will be made from the simulations on how these factors would have to interact with the chromatin fiber to exert their biological function. The results from the modeling and simulations and are expected to be highly relevant for a better understanding of gene expression regulation, since its is closely related to chromatin fiber conformation.

Simulated structures are vizualized using VRML-models for our publication in Biophysical Journal (Biophys. J., 95(8), p. 3677-3691, 2008).

Main researcher: Robert Schöpflin

This work was done in collaboration with the group Genome Organization & Function at Bioquant, Heidelberg.

This work was funded by Volkswagen-Foundation and by the German Ministry of Science and Education, partners of the ERASysBio+ initiative supported under the EU ERA-NET Plus scheme in FP7. Much of the computation was done on the Supercomputer of the North-German Supercomputing Alliance HLRN, Berlin/Hannover.

Modelling the Metastatic Cascade

In this project we develop a computer model which describes the dynamics of the dissemination of malignant cells and the possibilities of interventions.

Main researcher: Anja Bethge

This work is done in collaboration with the group Department of Anatomy II: Experimental Morphology at University Medical Center Hamburg-Eppendorf.

This work is funded by the Institute of Applied Computer Science (IACS) of the University of Applied Sciences Stralsund.

Former Projects

Molecular Computation Kit (MCK)

We developed a general framework for the computation of properties of biological macromolecules. Focus for the first increment was on properties of DNA.

This work was done in collaboration with the group Genome Organization & Function at Bioquant, Heidelberg.