"Ribonucleic acid (RNA) is acquiring a larger importance in cell biology, as more functions that it accomplishes are discovered. In particular, as it has emerged in the last decade, it has a crucial role in the post-transcriptional regulation of gene expression. The comprehension of these mechanisms and, in general, of RNA properties at a molecular level is a key issue in the study of many diseases and paves the way to possible applications in molecular medicine. Particularly interesting in this context are riboswitches, small portions of messenger RNAs which change their conformation in presence of specific metabolites and consequently inhibit or enhance gene transcription or translation. Another issue of paramount interest is RNA metabolism, crucial for viral replication, and in particular of the interaction of RNAs and the molecular motors devoted to its manipulation and unwinding. One of the goals of the present project is to develop new in silico approaches based on molecular dynamics for the study of small RNA molecules. In particular, the research will focus on (a) the development of ad hoc techniques to accelerate molecular dynamics simulations of RNA and of RNA-protein complexes and (b) to predict the three-dimensional structure of small RNAs. Another major goal of the present project is to apply the aforementioned techniques, in combination with standard molecular dynamics and state-of-the-art rare-event methods, to the study of three extremely relevant topics: (a) the interaction between RNA and the helicases, which are the enzymes devoted to its unwinding in the cell, (b) the conformational transitions in riboswitches, and (c) the structure of non-coding inverted short interspersed elements (SINE)."