The dynamics of single enzyme reactions: A reconsideration of Kramers' model for colored noise processes

Chaudhury, Srabanti and Chatterjee, Debarati and Cherayil, Binny J (2008) The dynamics of single enzyme reactions: A reconsideration of Kramers' model for colored noise processes. In: Journal of Chemical Physics, 129 (7). 075104-1-075104-7.

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Abstract

The utility of an approximate heuristic version of Kramers' theory of reaction rates that was earlier used [Chaudhury and Cherayil, J. Chem. Phys. 125, 024904 (2006)] to successfully describe the nonexponential waiting time distributions of the enzyme \beta -galactosidase is reassessed. The original model, based on the Smoluchowski equation, is reformulated in terms of the phase space variables of the reaction coordinate, without neglecting inertial contributions. A new derivation of the Fokker- lanck equation (FPE) that describes the dynamics of this coordinate is presented. This derivation, based on functional methods, provides a more direct alternative to the existing distribution function approach used by Hanggi and Mojtabai [Phys. Rev. A 26, 1168 (1982)]. The time-dependent coefficients in the FPE, when incorporated into the exact expression for the transmission coefficient obtained from a reactive-flux formalism [Kohen and Tannor, J. Chem. Phys. 103, 6013 (1995)], are found to yield virtually the same results as the earlier heuristic model.

Item Type:	Journal Article
Publication:	Journal of Chemical Physics
Publisher:	American Institute of Physics
Additional Information:	Copyright of this article belongs to American Institute of Physics.
Department/Centre:	Division of Chemical Sciences > Inorganic & Physical Chemistry
Date Deposited:	25 Sep 2008 07:16
Last Modified:	19 Sep 2010 04:50
URI:	http://eprints.iisc.ac.in/id/eprint/15994

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