Literature DB >> 19905097

Competition between multiple totally asymmetric simple exclusion processes for a finite pool of resources.

L Jonathan Cook1, R K P Zia, B Schmittmann.   

Abstract

Using Monte Carlo simulations and a domain-wall theory, we discuss the effect of coupling several totally asymmetric simple exclusion processes (TASEPs) to a finite reservoir of particles. This simple model mimics directed biological transport processes in the presence of finite resources such as protein synthesis limited by a finite pool of ribosomes. If all TASEPs have equal length, we find behavior which is analogous to a single TASEP coupled to a finite pool. For the more generic case of chains with different lengths, several unanticipated regimes emerge. A generalized domain-wall theory captures our findings in good agreement with simulation results.

Year:  2009        PMID: 19905097     DOI: 10.1103/PhysRevE.80.031142

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


  10 in total

1.  Mixed population of competing totally asymmetric simple exclusion processes with a shared reservoir of particles.

Authors:  Philip Greulich; Luca Ciandrini; Rosalind J Allen; M Carmen Romano
Journal:  Phys Rev E Stat Nonlin Soft Matter Phys       Date:  2012-01-27

2.  The molecular aetiology of tRNA synthetase depletion: induction of a GCN4 amino acid starvation response despite homeostatic maintenance of charged tRNA levels.

Authors:  Matthew R McFarland; Corina D Keller; Brandon M Childers; Stephen A Adeniyi; Holly Corrigall; Adélaïde Raguin; M Carmen Romano; Ian Stansfield
Journal:  Nucleic Acids Res       Date:  2020-04-06       Impact factor: 16.971

3.  Predictive biophysical modeling and understanding of the dynamics of mRNA translation and its evolution.

Authors:  Hadas Zur; Tamir Tuller
Journal:  Nucleic Acids Res       Date:  2016-09-02       Impact factor: 16.971

4.  Role of the particle's stepping cycle in an asymmetric exclusion process: a model of mRNA translation.

Authors:  L Ciandrini; I Stansfield; M C Romano
Journal:  Phys Rev E Stat Nonlin Soft Matter Phys       Date:  2010-05-05

5.  Limited resources in a driven diffusion process.

Authors:  Chris A Brackley; M Carmen Romano; Celso Grebogi; Marco Thiel
Journal:  Phys Rev Lett       Date:  2010-08-11       Impact factor: 9.161

6.  The dynamics of supply and demand in mRNA translation.

Authors:  Chris A Brackley; M Carmen Romano; Marco Thiel
Journal:  PLoS Comput Biol       Date:  2011-10-13       Impact factor: 4.475

Review 7.  Mathematical and Computational Modelling of Ribosomal Movement and Protein Synthesis: an overview.

Authors:  Tobias von der Haar
Journal:  Comput Struct Biotechnol J       Date:  2012-02-20       Impact factor: 7.271

8.  What determines eukaryotic translation elongation: recent molecular and quantitative analyses of protein synthesis.

Authors:  Nagammal Neelagandan; Irene Lamberti; Hugo J F Carvalho; Cédric Gobet; Felix Naef
Journal:  Open Biol       Date:  2020-12-09       Impact factor: 6.411

9.  Accelerating Whole-Cell Simulations of mRNA Translation Using a Dedicated Hardware.

Authors:  David Shallom; Danny Naiger; Shlomo Weiss; Tamir Tuller
Journal:  ACS Synth Biol       Date:  2021-11-23       Impact factor: 5.110

10.  Dynamics and growth rate implications of ribosomes and mRNAs interaction in E. coli.

Authors:  Tin Phan; Changhan He; Irakli Loladze; Clay Prater; Jim Elser; Yang Kuang
Journal:  Heliyon       Date:  2022-06-28
  10 in total

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