BIOPHYSICAL THEORY AND MODELING |
Effective Temperature in Stochastic Kinetics and Gene
Networks
Ting Lu 1, Jeff Hasty 1 and Peter G. Wolynes 1*
1 University of California, San Diego
* To whom correspondence should be addressed. E-mail: pwolynes{at}ucsd.edu.
Submitted on November 18, 2005
Revised on January 31, 2006
Accepted on 13 March 2006
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Abstract |
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The fluctuation-dissipation theorem, one of the central theorems in thermal dynamics, breaks down in out-of-Equilibrium systems. The idea of effective temperature coming from the extensions of that theorem has been recently introduced to study glasses and has proved to be a key concept for out-of-equilibrium systems. Gene networks involve stochastic chemical kinetics and are far from equilibrium. This leads us to try to use the notion of effective temperature to study them. To develop this idea, we study a simple birth-death process and a general two-species interacting process using the language of effective temperature. Further more, a model of a nonregulatory gene is studied as an example. The effective temperature may serves as an alternative and somewhat more fundamental language to describe the intrinsic-extrinsic noise distinction which has already provided a tool for qualifying gene networks.
Key Words:
effective temperature, fluctuation-dissipation theorem, gene networks, nonequilibrium, stochastic kinetics
