  Recently single molecule experiments have shown the importance of internal
friction in biopolymer dynamics. Such studies also suggested that the internal
friction although independent of solvent viscosity has strong dependence on
denaturant concentration. Recent simulations also support such propositions by
pointing out weak interactions to be the origin of internal friction in
proteins. Here we made an attempt to investigate how a single polymer chain
with internal friction undergoes reconfiguration and looping dynamics in a
confining potential which accounts for the presence of the denaturant, by using
recently proposed Compacted Rouse with internal friction (CRIF). We also
incorporated the effect of hydrodynamics by extending this further to Compacted
Zimm with internal friction (CZIF). All the calculations are carried out within
the Wilemski Fixmann (WF) framework. By changing the strength of the
confinement we mimicked chains with different degrees of compactness at
different denaturant concentrations. While compared with experiments our
results are found to be in good agreement.
