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The objective of this project was the development and performance optimisation of a coupling application. The coupler library is intended for interfacing massively-parallel algorithms for multi-physics simulations. The development of the coupler library adopted the same philosophy of the Message Passing Interface (MPI) library: The coupler was engineered as a set of libraries that are accessibl...

The use of time-dependent restraints in molecular simulation in order to generate a conformational ensemble for molecules that is in accordance with measured ensemble averages for particular observable quantities is investigated. Using a model system consisting of liquid butane and the cyclic peptide antamanide the reproduction of particular average (3) J-coupling constant values in a molecular...

Aptamers are nucleic acid molecules selected in vitro to bind small molecules, peptides, proteins or even other nucleic acids with high affinity and specificity. They offer a unique opportunity to extend our knowledge on the basic principles of nucleic acid architecture and ligand recognition. Despite their probable absence in organisms, RNA aptamers are likely to play an important role in mole...