Universität zu Köln

Ghosh, Soumendu, Mishra, Bhavya, Patra, Shubhadeep, Schadschneider, Andreas and Chowdhury, Debashish (2018). A biologically inspired two-species exclusion model: effects of RNA polymerase motor traffic on simultaneous DNA replication. J. Stat. Mech.-Theory Exp.. BRISTOL: IOP PUBLISHING LTD. ISSN 1742-5468

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Abstract

We introduce a two-species exclusion model to describe the key features of the conflict between the RNA polymerase (RNAP) motor traffic, engaged in the transcription of a segment of DNA, concomitant with the progress of two DNA replication forks on the same DNA segment. One of the species of particles (P) represents RNAP motors while the other (R) represents the replication forks. Motivated by the biological phenomena that this model is intended to capture, a maximum of two R particles only are allowed to enter the lattice from two opposite ends whereas the unrestricted number of P particles constitutes a totally asymmetric simple exclusion process (TASEP) in a segment in the middle of the lattice. The model captures three distinct pathways for resolving the co-directional as well as head-on collision between the P and R particles. Using Monte Carlo simulations and heuristic analytical arguments that combine exact results for the TASEP with mean-field approximations, we predict the possible outcomes of the conflict between the traffic of RNAP motors (P particles engaged in transcription) and the replication forks (R particles). In principle, the model can be adapted to experimental conditions to account for the data quantitatively.

Item Type:	Journal Article
Creators:	Creators Email ORCID ORCID Put Code Ghosh, Soumendu UNSPECIFIED UNSPECIFIED UNSPECIFIED Mishra, Bhavya UNSPECIFIED UNSPECIFIED UNSPECIFIED Patra, Shubhadeep UNSPECIFIED UNSPECIFIED UNSPECIFIED Schadschneider, Andreas UNSPECIFIED UNSPECIFIED UNSPECIFIED Chowdhury, Debashish UNSPECIFIED UNSPECIFIED UNSPECIFIED
URN:	urn:nbn:de:hbz:38-191371
DOI:	10.1088/1742-5468/aab021
Journal or Publication Title:	J. Stat. Mech.-Theory Exp.
Date:	2018
Publisher:	IOP PUBLISHING LTD
Place of Publication:	BRISTOL
ISSN:	1742-5468
Language:	English
Faculty:	Unspecified
Divisions:	Unspecified
Subjects:	no entry
Uncontrolled Keywords:	Keywords Language TRANSCRIPTION; CONFLICTS; PHYSICS; PHASE Multiple languages Mechanics; Physics, Mathematical Multiple languages
Refereed:	Yes
URI:	http://kups.ub.uni-koeln.de/id/eprint/19137