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Looping dynamics of a flexible chain with internal friction at different degrees of compactness

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Title Looping dynamics of a flexible chain with internal friction at different degrees of compactness
 
Creator SAMANTA, N
CHAKRABARTI, R
 
Subject DEPENDENT SURVIVAL PROBABILITY
DIFFUSION-CONTROLLED REACTIONS
PROTEIN-FOLDING RATES
POLYMER-CHAIN
SEMIFLEXIBLE POLYMERS
UNFOLDED PROTEIN
KINK MOTION
MOLECULE
VISCOSITY
SPECTROSCOPY
Brownian motion
Internal friction
Polymer dynamics
 
Description In recent times 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 a strong dependence on denaturant concentration. In addition, recent simulations showed that the weak interactions contribute to the internal friction in proteins. In this work we made an attempt to investigate how a single polymer chain with internal friction undergoes reconfiguration and looping dynamics in a confining potential that accounts for the presence of the denaturant, by using recently proposed "Compacted Rouse with internal friction". We also incorporated the effect of hydrodynamics by extending this further to "Compacted Zimm with internal friction". All the calculations are carried out within the Wilemski Fixman framework without invoking excluded-volume effect. 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. (C) 2015 Elsevier B.V. All rights reserved.
 
Publisher ELSEVIER SCIENCE BV
 
Date 2016-01-15T04:53:33Z
2016-01-15T04:53:33Z
2015
 
Type Article
 
Identifier PHYSICA A-STATISTICAL MECHANICS AND ITS APPLICATIONS, 436,377-386
0378-4371
1873-2119
http://dx.doi.org/10.1016/j.physa.2015.05.042
http://dspace.library.iitb.ac.in/jspui/handle/100/17807
 
Language en