The following pages features highlighs of projects currently supported by sciCORE:
Resistance to antibiotics is very rapidly increasing worldwide, and there are less and less new antibiotics developed. There is thus an urgent and unmet medical need for the development of innovative approaches to treat infectious diseases. TargetInfectX aims at using RNA interference (RNAi) by small inhibitory RNAs (siRNAs) to (i) identify human proteins as general targets for anti-infective intervention and (ii) to evaluate the potency of specific siRNAs for anti-infective treatment. sciCORE supports the project by providing large scale storage, HPC resources for image analysis and hosting scientific programmers in the team.
Prof. Christoph Dehio - website
The potassium channels constitute a large family of membrane proteins playing a key role in the function of neurons. The activity of a potassium channel is mainly determined by its intrinsic conductance and various gating mechanisms and will be described by a Markovian state model. Transition rates will be extracted from the scientific literature by curators from the Swiss-Prot team and from molecular mechanics simulations performed by Dr Bernèche. Homology models built by the SWISS-Model team will be combined with the above information to identify key structural motifs allowing us to estimate missing rate constants in the different Markovian models.Finally these Markovian state models will serve as the basis for computationally more efficient analytical models of channel kinetics that can be incorporated in neuronal simulations. These analytical models should be much more complete, incorporating the effects of many external factors on the activity of different potassium channels, than the current simulation frameworks which rely mainly on the Hodgkin-Huxley formalism. This research is partly done in the context of the Human Brain Project.
Dr Simon Bernèche
Simulation methods are a powerful tool to determine the structure and electronic properties of condensed matter systems. Due to the rapidly increasing speed of computers, simulation is a very active field with many opportunities to improve simulation methods and with new applications becoming feasible. We develop better algorithms for such atomistic calculations and apply them to challenging problems. The research has interdisciplinary character, involving physics, mathematics, chemistry and computer science. The picture shows the lowest energy point defect in silicon. Our simulation (Goedecker et al., Phys. Rev. Lett. 88, 235501 (2002)) reveals the atomic positions (large spheres) and the bond centers (small blue spheres). Two silicon atoms that were in the crystalline bulk in the positions denoted by the black spheres moved to the positions given by the red spheres.
Prof. Stefan Goedecker - website
Deficits in memory are implicated in a large variety of psychiatric diseases. Hence deciphering molecular pathways of memory while making use of psychological as well as biological knowledge yields a promising approach in advancing our understanding of these diseases and the functioning of the human brain. The project aims at connecting findings from molecular biology with human behavior, especially episodic memory.
Prof. Andreas Papassotiropoulos - website