At the eScience Center we can provide the support you need to solve large, advanced, complex computational problems which are too big for a single machine to compute.

Check out the below videos for more information.

Faculty of Science – Department of Physics, Chemistry and Pharmacy (FKF) – SDU

Migratory songbirds can perceive the Earth’s magnetic field for the purpose of navigating their exceptional voyages or orienting in their local habitats. One particular modality of this sense, a magnetic inclination compass, is thought to rely on magnetically sensitive radical pairs formed photochemically in cryptochrome proteins in the animal’s retinae. This process is a striking example of a truly quantum mechanical process in sensory biology. It necessitates long-lived electron spin coherences in the radical pair.

An important requirement of this hypothesis is that the electron spin relaxation is slow enough for the Earth’s magnetic field to have a significant effect on the coherent spin dynamics of the transient radical pair. This proposal aims to elucidate spin relaxation pathways based on a comprehensive analysis of the thermally induced motions in the radicals and their surroundings.

Faculty of Science – Department of Mathematics and Computer Science (IMADA) – SDU

For an evaluation study on unsupervised outlier detection and ensemble techniques, we run various methods with various parameterizations on many datasets, resulting in ca. 4.5 mio. individual experiments which are to a certain extent independent of each other and try to see what the benefits of parallelization are on this effort.

Faculty of Science – Department of Physics, Chemistry and Pharmacy (FKF) – SDU

The aim of this project is to rethink the current standard colorectal cancer (CRC) screening program Computational chemistry is emerging as an extremely powerful addition to the experimental tool box of chemistry and biology. Calculations performed on HPC systems have the potential to both explain and guide experiments. In this project, we use computational methods to study the structure and stability of chemically engineered nucleic acid duplexes as well as to study a key process in the synthesis of the bacterial cell wall. The projects will provide new insight and understanding at an atomic level.

Faculty of Science – Department of Physics, Chemistry and Pharmacy (FKF) – SDU

Gels made of stiff polymers are of interest for multiple reasons. Fundamentally, their topological entanglement properties are quite different from dens melts of flexible chains, secondly many biomaterials such as f-actin gels are composed of stiff biological polymers. Computationally, naively simulating stiff polymers with bead-spring models are expensive, since stiff chains require angular potentials with high spring strengths, and hence require small time steps, and many beads are required to decorate the chain. Recently, it became possible to add pair interactions not between beads, but between the bonds connecting beads. Such interactions allow for computationally much more effective models of stiff polymer gels, since much fewer beads are required to model a stiff polymer. Secondly, the bond pair interactions can be designed to ensure gel topology is conserved. In the present project, we investigate and benchmark how to apply these computational techniques and optionally how to map the gel models onto biological gel systems.

Faculty of Science – Department of Physics, Chemistry and Pharmacy (FKF) – SDU

We are interested in the molecular and biophysical processes occurring in proteins and membranes. We use highly parallel numerical integrators to study the self-assembly and dynamic behaviour of biological complexes that drive life. Such highly parallel computations are only possible on large scale HPC resources, because we study the dynamics of millions of particles, which cannot be performed on desktop computers. Using our computations, we have discovered new transport pathways across cellular membranes, have examined the dynamics and mechanical properties of the Zika virus, and describe the molecular processes involved in the formation of organelles that control fat metabolism.

Faculty of Science – Department of Physics, Chemistry and Pharmacy (FKF) – SDU

We develop and apply quantum chemical methods to study biological systems. We are especially interested in defining rational design strategies for development of novel functional optical biological materials relevant for example for light-harvesting and biological sensing. For our research, use of supercomputers like ABACUS 2.0 is of utmost importance – such computing facilities represent our laboratory and this is where we do our experiments using the computational strategies we develop.

Faculty of Science – Department of Mathematics and Computer Science (IMADA) – SDU

In this project we study the three-dimensional folding structure of RNA molecules. Understanding folding of RNA is important as wrongly folded molecules could lead to serious diseases. We use a computer simulation method called “molecular dynamics” for studying the physical movements of atoms and molecules. On ABACUS2.0 molecules are represented as 3-dimensional geometrical data and a single simulation of one experiment requires about 7000 simulation steps. This method requires a tremendous amount of computer simulations and it can take many years on a normal computer to complete only one experiment.