Pausing and backtracking in transcription under dense traffic conditions

DOI10.1007/S10955-011-0120-3MaRDI QIDQ540563zbMATHOpenAlexWikidataFDO

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

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

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Cites work

• scientific article; zbMATH DE number 841532 (Why is no real title available?)
• Exact solution of a 1D asymmetric exclusion model using a matrix formulation
• 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

(12)

• 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
• Deterministic and stochastic descriptions of gene expression dynamics
• A biologically inspired two-species exclusion model: effects of RNA polymerase motor traffic on simultaneous DNA replication
• Cooperative and sequence-dependent model for RNAP dynamics: application to ribosomal gene transcription
• On the distribution of transcription times
• RNA polymerase interactions and elongation rate
• 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
• Dynamics of transcription of closely spaced promoters in \textit{Escherichia coli}, one event at a time
• Ultradiscrete modeling and simulation for gene transcription

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