Our research aims at quantitatively understanding the structural and dynamical mechanism of biomolecular folding and function in computer simulations. We focus on systems of high biological relevance in the context of genetic regulation, among them Two-Component Signal Transduction Systems and regulatory ncRNA like Riboswitches. A typical challenge in these simulations is reaching sufficiently long timescales while maintaining a realistic description of the system. We therefore develop novel computational tools in a multi-scaling approach and combine efficient sampling techniques at a coarse-grained level of description with more expensive detailed models. Ultimately, the knowledge gained on the biomolecular systems might find application in synthetic biology or pharmacology by controlling genetic regulation and help develop modules for synthetic biology.