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Internal friction in polymers:

Loop formation in long chain molecules is a primary step in polypeptide, protein folding as well as in processes like DNA transcription. We have recently looked at the effect of hydrodynamic interaction on end-to-end loop formation in flexible polymer. We have shown how hydrodynamics can actually make loop formation faster. On the other hand, in a separate study, we have shown that the presence of viscoelastic solvent around the chain makes looping dynamics slow. Very recently we have analyzed how internal friction can influence end-to-end looping dynamics. We have also analyzed how fluctuating hydrodynamics in addition to internal viscosity affect the dynamics in a dumbbell model for polymer chain. Our recent work dealt with the use of Jarzynski equality to measure the internal friction of a polymer from optical tweezer experiments. A future problem would be to come up with a multi-chain code to model real dilute polymer solution and investigate the combined effect of hydrodynamics and internal viscosity on dynamics.


Relevant Publications:

1. Shear viscosity for finitely extensible chains with fluctuating internal friction and hydrodynamic interactions - R. Kailasham,  Rajarshi Chakrabarti and J. Ravi Prakash, J. Rheol. 67, 105 (2023).


2. How important are fluctuations in the treatment of internal friction in polymers? - R. Kailasham,  Rajarshi Chakrabarti and J. Ravi Prakash, Soft Matter 17, 7133 (2021).

3. Rouse model with fluctuating internal friction - R. Kailasham, Rajarshi Chakrabarti and J. Ravi Prakash J. Rheol. 65, 903 (2021).

4. Wet and dry internal friction can be measured with the Jarzynski equality - R. Kailasham, Rajarshi Chakrabarti and J. Ravi Prakash, Phys. Rev. Res. 2, 013331 (2020).

5. Rheological consequences of wet and dry friction in a dumbbell model with hydrodynamic interactions and internal viscosity  - R. Kailasham, Rajarshi Chakrabarti and J. Ravi Prakash, J. Chem. Phys. 149, 094903 (2018). (This article has been selected as a 2018 Editors' Choice article).

6. Reconfiguration Dynamics in folded and intrinsically disordered protein with internal friction: Effect of solvent quality and denaturant - Nairhita Samanta and Rajarshi Chakrabarti, Physica A: Statistical Mechanics and its Applications 450, 165 (2016).

7. Looping Dynamics of a flexible chain with internal friction at different degrees of compactness - Nairhita Samanta and Rajarshi Chakrabarti, Physica A: Statistical Mechanics and its Applications 436, 377 (2015).

8. Looping and reconfiguration dynamics of a flexible chain with internal friction - Nairhita Samanta, Jayanta Ghosh and Rajarshi Chakrabarti,  AIP Adv. 4, 067102 (2014).

9. End to end loop formation in a single polymer chain with internal friction - Nairhita Samanta and Rajarshi Chakrabarti, Chem. Phys. Letts. 582, 71 (2013).

Conference Proceedings:

1. How does the tail length and separation between the tagged monomers influence the reconfiguration of a chain with internal friction for different solvent-quality? - Nairhita Samanta and Rajarshi Chakrabarti, J. Phys : Conf. Ser 759, 012014 (2016).

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