Effective temperature in stochastic kinetics and gene networks.

Biophysical Journal
Ting LuPeter G Wolynes

Abstract

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. Furthermore, 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 that has already provided a tool for qualifying gene networks.

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Citations

Jul 4, 2012·Nature Structural & Molecular Biology·Zach HenselJie Xiao
Nov 21, 2007·Proceedings of the National Academy of Sciences of the United States of America·Ting LuJeff Hasty
Sep 18, 2007·The Journal of Chemical Physics·Yurie OkabeMasaki Sasai
Aug 10, 2011·The Journal of Chemical Physics·Shenshen Wang, Peter G Wolynes
Oct 27, 2010·Journal of Theoretical Biology·Bo LiuQi Wang
Jun 17, 2016·Journal of the Royal Society, Interface·Marc Weber, Javier Buceta
Oct 18, 2006·The Journal of Chemical Physics·Patrick B WarrenPieter Rein ten Wolde
Jan 18, 2018·Integrative Biology : Quantitative Biosciences From Nano to Macro·Chunhe Li
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Jul 23, 2008·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Davide LoiLeticia F Cugliandolo
Aug 14, 2008·Physical Biology·Ting LuJeff Hasty
Apr 7, 2010·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Gerardo Aquino, Robert G Endres
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Jul 25, 2008·American Journal of Physiology. Cell Physiology·Carolyn L BullerFrank C Brosius
Jan 22, 2021·The Journal of Physical Chemistry. B·Jia-Liang ShenPeter G Wolynes
Feb 8, 2018·Biophysical Journal·Andrew E BlanchardTing Lu
May 17, 2012·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Haidong FengJin Wang

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