Ribosome flow model with nonhomogeneous site sizes

Eyal Bar-Shalom, Alexander Ovseevich, Michael Margaliot

Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

Abstract

We introduce and analyze two general dynamical models for unidirectional movement of particles along a circular and an open chain of sites. The models include a soft version of the simple exclusion principle, thus allowing to model and analyze the evolution of traffic jams of particles along the chain. A unique feature of these two new models is that each site along the chain may have a different size. Although nonlinear, the models are amenable to rigorous analysis. We prove that the dynamics always converges to a steady-state, and that the steady-state densities along the chain and the steady-state output flow rate can be derived from the spectral properties of a suitable matrix, thus eliminating the need to numerically simulate the dynamics until convergence. This spectral representation also allows for powerful sensitivity analysis, i.e. understanding how a change in one of the parameters affects the steady-state. The site sizes and the transition rates from site to site play different roles in the dynamics, and for the purpose of maximizing the steady-state output (or production) rate the site sizes are more important than the transition rates. The new models can be applied to study various natural and artificial systems including networks of ribosome flow during mRNA translation, phosphorelay, the movement of molecular motors along filaments of the cytoskeleton, and pedestrian and vehicular traffic.

Original languageEnglish
Title of host publication2019 IEEE 58th Conference on Decision and Control, CDC 2019
PublisherInstitute of Electrical and Electronics Engineers Inc.
Pages25-30
Number of pages6
ISBN (Electronic)9781728113982
DOIs
StatePublished - Dec 2019
Event58th IEEE Conference on Decision and Control, CDC 2019 - Nice, France
Duration: 11 Dec 201913 Dec 2019

Publication series

NameProceedings of the IEEE Conference on Decision and Control
Volume2019-December
ISSN (Print)0743-1546
ISSN (Electronic)2576-2370

Conference

Conference58th IEEE Conference on Decision and Control, CDC 2019
Country/TerritoryFrance
CityNice
Period11/12/1913/12/19

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