Pausing and backtracking in transcription under dense traffic conditions

DOI10.1007/S10955-011-0120-3MaRDI QIDQ540563zbMATH OpenOpenAlexWikidataFDO

Authors Stefan Klumpp

Publication date 3 June 2011

Published in Journal of Statistical Physics (Search for Journal in Brave)

Full work available at URL https://doi.org/10.1007/s10955-011-0120-3

zbMATH Keywords

cooperativityexclusion processRNA polymerasetraffic models

Mathematics Subject Classification ID

Lattice systems (Ising, dimer, Potts, etc.) and systems on graphs arising in equilibrium statistical mechanics (82B20) Random walks, random surfaces, lattice animals, etc. in equilibrium statistical mechanics (82B41) Protein sequences, DNA sequences (92D20)

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Cites work

• Exact solution of a 1D asymmetric exclusion model using a matrix formulation
• scientific article; zbMATH DE number 841532 (Why is no real title available?)
• Phase diagram of one-dimensional driven lattice gases with open boundaries
• Phase transitions in an exactly soluble one-dimensional exclusion process
• Totally asymmetric exclusion processes with particles of arbitrary size
• Towards a model for protein production rates

Cited in

(13)

• RNA polymerase interactions and elongation rate
• Dynamics of transcription of closely spaced promoters in \textit{Escherichia coli}, one event at a time
• Deterministic and stochastic descriptions of gene expression dynamics
• Bi-directional traffic of molecular motors in two antiparallel lanes with asymmetric lane changing rates
• Operon dynamics with state dependent transcription and/or translation delays
• Cooperative and sequence-dependent model for RNAP dynamics: application to ribosomal gene transcription
• A traffic flow model for bio-polymerization processes
• A multispecies exclusion model inspired by transcriptional interference
• First-passage processes on a filamentous track in a dense traffic: optimizing diffusive search for a target in crowding conditions
• A biologically inspired two-species exclusion model: effects of RNA polymerase motor traffic on simultaneous DNA replication
• Ultradiscrete modeling and simulation for gene transcription
• On the distribution of transcription times
• A numerical study of a stabilized hyperbolic equation inspired by models for bio-polymerization

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