Confinement and viscoelastic effects on chain closure dynamics

Bhattacharyya, Pinaki and Sharma, Rati and Cherayil, Binny J (2012) Confinement and viscoelastic effects on chain closure dynamics. In: JOURNAL OF CHEMICAL PHYSICS, 136 (23).

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Abstract

Chemical reactions inside cells are typically subject to the effects both of the cell's confining surfaces and of the viscoelastic behavior of its contents. In this paper, we show how the outcome of one particular reaction of relevance to cellular biochemistry - the diffusion-limited cyclization of long chain polymers - is influenced by such confinement and crowding effects. More specifically, starting from the Rouse model of polymer dynamics, and invoking the Wilemski-Fixman approximation, we determine the scaling relationship between the mean closure time t(c) of a flexible chain (no excluded volume or hydrodynamic interactions) and the length N of its contour under the following separate conditions: (a) confinement of the chain to a sphere of radius d and (b) modulation of its dynamics by colored Gaussian noise. Among other results, we find that in case (a) when d is much smaller than the size of the chain, t(c) similar to Nd-2, and that in case (b), t(c) similar to N-2/(2 (2H)), H being a number between 1/2 and 1 that characterizes the decay of the noise correlations. H is not known a priori, but values of about 0.7 have been used in the successful characterization of protein conformational dynamics. At this value of H (selected for purposes of illustration), t(c) similar to N-3.4, the high scaling exponent reflecting the slow relaxation of the chain in a viscoelastic medium. (C) 2012 American Institute of Physics. http://dx.doi.org/10.1063/1.4729041]

Item Type:	Journal Article
Publication:	JOURNAL OF CHEMICAL PHYSICS
Publisher:	AMER INST PHYSICS
Additional Information:	Copy right for this article belongs to American Institute of Physics
Department/Centre:	Division of Chemical Sciences > Inorganic & Physical Chemistry
Date Deposited:	06 Aug 2012 07:20
Last Modified:	06 Aug 2012 07:21
URI:	http://eprints.iisc.ac.in/id/eprint/44926

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