Our research aims at quantitatively understanding the structural and dynamical molecular mechanism of genetic regulation in HPC computer simulations. We want to connect method development directly with life-science applications and focus on systems of high biological relevance in the context of genetic regulation. Examples of such system which we currently investigate are Two-Component Signal Transduction Systems and regulatory ncRNA like Riboswitches or the group II intron. The challenge in simulating these systems is reaching sufficiently long time-scales while maintaining a realistic description. We therefore develop high-performance computational tools which apply a multi-scaling approach, in which we combine efficient sampling techniques at a coarse-grained level of description with more expensive but more detailed models. Ultimately, the knowledge gained on the biomolecular systems might find application in synthetic biology or pharmacology, by controlling their genetic regulation and helping development modules for synthetic biology.