Research

Our Research

ESPResSo

ESPResSo is a free, open-source software package for simulations of soft-matter systems, which is co-developed and used in the working group for most of its research.

ESPResSo is capable of doing classical Molecular dynamics simulations of many types of systems in different statistical ensembles (NVE, NVT, NPT). It contains many advanced simulation algorithms like Lattice-Boltzmann, electrostatics, electrokinetics, dipolar interactions, electrophoresis, catalytic reactions and many more. ESPResSo is controlled via Python scripts, which gives it a great flexibility.

Besides doing the regular research on different physical systems, the working group is constantly trying to improve and extend the ESPResSo software. The developement follows continuous integration practice and is active on github.

Algorithms for Long Range Interactions

A potential is defined to be short ranged if it decreases with distance  r quicker or similar than r^{-(d-1)} where  d is the dimensionality of the system. Electrostatic, gravitatory and dipolar interactions, present in many physical systems, are examples of long range interactions. When long range intgeractions are present in a system, the weight of the interactions comming from far particles is non negligible

Algorithms for Long Range Interactions

DNA Electrophoresis

Electrophoresis is one of the main techniques to separate DNA molecules by size and has shown its effectiveness in the sequencing of entire genomes, including our own. This success story also increased the demand for improved and faster sequencing methods, in order to meet the upcoming challenges.

More recently, the DNA has been investigated as a material for the self assembly of complex three dimensional structures. These structures have been investigated in the scientific community as a material for drug delivery or nanomachines. However, even the fundamental understanding of the ion dynamics in electric field driven nanopore translocation of such structures is not fully understood yet. Such systems are therefore investigated via a multi-scale approach from all-atom models to mean-field models. 

Nanopore Sequencing

Biological macromolecules are indispensable for the human body. They serve as energy sources, metabolic helpers, tiny "robots" or means of communication and are crucial for many metabolic processes. Researching them helps to understand diseases and develop medicines more precisely.

Over the last ten years, researchers have developed methods to accurately sequence DNA and RNA at the molecular level. The nanodiag BW future cluster is now endeavouring to extend these techniques to proteins and peptides.

The substance to be analysed is placed in a salt solution that is separated by a lipid membrane with a nanopore. This pore enables the transport of atoms, ions and molecules. An applied electrical voltage causes the transport of ions and the analyte through the pore. The interaction of the analyte in the pore leads to a temporary reduction in the ion current, which is used for the analysis.

More information on Nanopore Sequencing

Contact

This image shows Christian Holm

Christian Holm

Prof. Dr.

Head of Institute

This image shows Simone Blümlein

Simone Blümlein

 

Administration

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