Interference of two co-directional exclusion processes in the presence of a static bottleneck: a biologically motivated model

Abstract

We develope a two-species exclusion process with a distinct pair of entry and exit sites for each species of rigid rods. The relatively slower forward stepping of the rods in an extended bottleneck region, located in between the two entry sites, controls the extent of interference of the co-directional flow of the two species of rods. The relative positions of the sites of entry of the two species of rods with respect to the location of the bottleneck are motivated by a biological phenomenon. However, the primary focus of the study here is to explore the effects of the interference of the flow of the two species of rods on their spatio-temporal organization and the regulations of this interference by the extended bottleneck. By a combination of mean-field theory and computer simulation we calculate the flux of both species of rods and their density profiles as well as the composite phase diagrams of the system. If the bottleneck is sufficiently stringent some of the phases become practically unrealizable although not ruled out on the basis of any fundamental physical principle. Moreover the extent of suppression of flow of the downstream entrants by the flow of the upstream entrants can also be regulated by the strength of the bottleneck. We speculate on the possible implications of the results in the context of the biological phenomenon that motivated the formulation of the theoretical model.

This is an author-created, un-copyedited final preprint version of an article published in Physical Review E (APS)

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• Trapping in bottlenecks: interplay between microscopic dynamics and large scale effects
• A Multispecies Exclusion Process with Fusion and Fission of Rods: a model inspired by Intraflagellar Transport
• A Biologically Motivated Asymmetric Exclusion Process: interplay of congestion in RNA polymerase traffic and slippage of nascent transcript