  In contrast to proteins much less attention has been focused on development
of computational models for describing RNA molecules, which are being
recognized as playing key roles in many cellular functions. Current atomically
detailed force fields are not accurate enough to capture the properties of even
simple nucleic acid constructs. In this article, we review our efforts to
develop coarse-grained (CG) models that capture the underlying physics for the
particular length scale of interest. Two models are discussed. One of them is
the Three Interaction Site (TIS) model in which each nucleotide is represented
by three beads corresponding to sugar, phosphate, and base. The other is the
Self-Organized Polymer (SOP) model in which each nucleotide is represented as a
single interaction center. Applications of the TIS model to study the
complexity of hairpin formation and the effects of crowding in shifting
equilibrium between two conformations in human telomerase pseudoknot are
described. The work on crowding illustrates a direct link to the activity of
telomerase. We use the SOP model to describe the response of {\it Tetrahymena}
ribozyme to force. The simulated unfolding pathways agree well with single
molecule pulling experiments. We also review predictions for the unfolding
pathways for {\it Azoarcus} ribozyme. The success of the CG applications to
describe dynamics in RNA gives hope that more complex processes involving
RNA-protein interactions can be tackled using variants of the proposed models.

Biomolecules;Soft Condensed Matter