Literature DB >> 19905366

Ubiquitous "glassy" relaxation in catalytic reaction networks.

Akinori Awazu1, Kunihiko Kaneko.   

Abstract

Study of reversible catalytic reaction networks is important not only as an issue for chemical thermodynamics but also for protocells. From extensive numerical simulations and theoretical analysis, slow relaxation dynamics to sustain nonequlibrium states are commonly observed. These dynamics show two types of salient behaviors that are reminiscent of glassy behavior: slow relaxation along with the logarithmic time dependence of the correlation function and the emergence of plateaus in the relaxation-time course. The former behavior is explained by the eigenvalue distribution of a Jacobian matrix around the equilibrium state that depends on the distribution of kinetic coefficients of reactions. The latter behavior is associated with kinetic constraints rather than metastable states and is due to the absence of catalysts for chemicals in excess and the negative correlation between two chemical species. Examples are given and generality is discussed with relevance to bottleneck-type dynamics in biochemical reactions as well.

Mesh:

Year:  2009        PMID: 19905366     DOI: 10.1103/PhysRevE.80.041931

Source DB:  PubMed          Journal:  Phys Rev E Stat Nonlin Soft Matter Phys        ISSN: 1539-3755


  7 in total

1.  Optimizing ring assembly reveals the strength of weak interactions.

Authors:  Eric J Deeds; John A Bachman; Walter Fontana
Journal:  Proc Natl Acad Sci U S A       Date:  2012-01-30       Impact factor: 11.205

2.  Generic temperature compensation of biological clocks by autonomous regulation of catalyst concentration.

Authors:  Tetsuhiro S Hatakeyama; Kunihiko Kaneko
Journal:  Proc Natl Acad Sci U S A       Date:  2012-05-07       Impact factor: 11.205

3.  Reaction dynamics analysis of a reconstituted Escherichia coli protein translation system by computational modeling.

Authors:  Tomoaki Matsuura; Naoki Tanimura; Kazufumi Hosoda; Tetsuya Yomo; Yoshihiro Shimizu
Journal:  Proc Natl Acad Sci U S A       Date:  2017-02-06       Impact factor: 11.205

4.  An Analytical Framework for Studying Small-Number Effects in Catalytic Reaction Networks: A Probability Generating Function Approach to Chemical Master Equations.

Authors:  Masaki Nakagawa; Yuichi Togashi
Journal:  Front Physiol       Date:  2016-03-24       Impact factor: 4.566

5.  Kinetic memory based on the enzyme-limited competition.

Authors:  Tetsuhiro S Hatakeyama; Kunihiko Kaneko
Journal:  PLoS Comput Biol       Date:  2014-08-14       Impact factor: 4.475

6.  Short relaxation times but long transient times in both simple and complex reaction networks.

Authors:  Adrien Henry; Olivier C Martin
Journal:  J R Soc Interface       Date:  2016-07       Impact factor: 4.118

7.  Dynamics robustness of cascading systems.

Authors:  Jonathan T Young; Tetsuhiro S Hatakeyama; Kunihiko Kaneko
Journal:  PLoS Comput Biol       Date:  2017-03-13       Impact factor: 4.475

  7 in total

北京卡尤迪生物科技股份有限公司 © 2022-2023.