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• W3099403710 abstract "Loop formation between monomers in the interior of semiflexible chains describes elementary events in biomolecular folding and DNA bending. We calculate analytically the interior distance distribution function for semiflexible chains using a mean field approach. Using the potential of mean force derived from the distance distribution function we present a simple expression for the kinetics of interior looping by adopting Kramers theory. For the parameters, that are appropriate for DNA, the theoretical predictions in comparison with the case are in excellent agreement with explicit Brownian dynamics simulations of wormlike chain (WLC) model. The interior looping times (τIC) can be greatly altered in the cases when the stiffness of the loop differs from that of the dangling ends. If the dangling end is stiffer than the loop then τIC increases for the case of the WLC with uniform persistence length. In contrast, attachment of flexible dangling ends enhances rate of interior loop formation. The theory also shows that if the monomers are charged and interact via screened Coulomb potential then both the cyclization (τc) and interior looping (τIC) times greatly increase at low ionic concentration. Because both τc and τIC are determined essentially by the effective persistence length [lp(R)] we computed lp(R) by varying the range of the repulsive interaction between the monomers. For short range interactions lp(R) nearly coincides with the bare persistence length which is determined largely by the backbone chain connectivity. This finding rationalizes the efficacy of describing a number of experimental observations (response of biopolymers to force and cyclization kinetics) in biomolecules using WLC model with an effective persistence length." @default.
• W3099403710 created "2020-11-23" @default.
• W3099403710 creator A5026267803 @default.
• W3099403710 creator A5036725653 @default.
• W3099403710 date "2006-03-14" @default.
• W3099403710 modified "2023-09-23" @default.
• W3099403710 title "Kinetics of interior loop formation in semiflexible chains" @default.
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• W3099403710 doi "https://doi.org/10.1063/1.2178805" @default.
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