  Using coarse-grained model we have explored forced-unfolding of RNA hairpin
as a function of $f_S$ and the loading rate ($r_f$). The simulations and
theoretical analysis have been done without and with the handles that are
explicitly modeled by semiflexible polymer chains. The mechanisms and time
scales for denaturation by temperature jump and mechanical unfolding are vastly
different. The directed perturbation of the native state by $f_S$ results in a
sequential unfolding of the hairpin starting from their ends whereas thermal
denaturation occurs stochastically. From the dependence of the unfolding rates
on $r_f$ and $f_S$ we show that the position of the unfolding transition state
(TS) is not a constant but moves dramatically as either $r_f$ or $f_S$ is
changed. The TS movements are interpreted by adopting the Hammond postulate for
forced-unfolding. Forced-unfolding simulations of RNA, with handles attached to
the two ends, show that the value of the unfolding force increases (especially
at high pulling speeds) as the length of the handles increases. The pathways
for refolding of RNA from stretched initial conformation, upon quenching $f_S$
to the quench force $f_Q$, are highly heterogeneous. The refolding times, upon
force quench, are at least an order of magnitude greater than those obtained by
temperature quench. The long $f_Q$-dependent refolding times starting from
fully stretched states are analyzed using a model that accounts for the
microscopic steps in the rate limiting step which involves the trans to gauche
transitions of the dihedral angles in the GAAA tetraloop. The simulations with
explicit molecular model for the handles show that the dynamics of force-quench
refolding is strongly dependent on the interplay of their contour length and
the persistence length, and the RNA persistence length.
