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Recently single molecule experiments have shown the importance of internalfriction in biopolymer dynamics. Such studies also suggested that the internalfriction although independent of solvent viscosity has strong dependence ondenaturant concentration. Recent simulations also support such propositions bypointing out weak interactions to be the origin of internal friction inproteins. Here we made an attempt to investigate how a single polymer chainwith internal friction undergoes reconfiguration and looping dynamics in aconfining potential which accounts for the presence of the denaturant, by usingrecently proposed Compacted Rouse with internal friction (CRIF). We alsoincorporated the effect of hydrodynamics by extending this further to CompactedZimm with internal friction (CZIF). All the calculations are carried out withinthe Wilemski Fixmann (WF) framework. By changing the strength of theconfinement we mimicked chains with different degrees of compactness atdifferent denaturant concentrations. While compared with experiments ourresults are found to be in good agreement.

Looping dynamics of flexible chain with internal friction at different degree of compactness