Chain decay and rates disorder in the totally asymmetric simple exclusion process

Yahaya Ibrahim; Jérôme Dorignac; Fred Geniet; Carole Chevalier; Jean-Charles Walter; Nils-Ole Walliser; Andrea Pameggiani; John Palmeri

arXiv · 2310.00329

Chain decay and rates disorder in the totally asymmetric simple exclusion process

Yahaya Ibrahim·Jérôme Dorignac·Fred Geniet·Carole Chevalier·Jean-Charles Walter·Nils-Ole Walliser·Andrea Pameggiani·John Palmeri

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Abstract

We theoretically study the Totally Asymmetric Exclusion Process (TASEP) with quenched jumping rates disorder and finite lifetime chain. TASEP is widely used to model the translation of messenger RNAs by Ribosomes in protein synthesis. Since the exact solution of the TASEP model is analytically and computationally intractable for biologically relevant systems parameters, the canonical Mean-Field (MF) approaches of solving coupled non-linear differential equations is also computational expensive for the scale of relevant biological data analysis. In this article, we provide alternative approach to computing the MF steady state solution via a computationally efficient system of non-linear algebraic equations. We further outline a framework for including correlations progressively via the exact solution of small size TASEP system. Leading order approximation in the biologically relevant entry rate limited regime shows remarkable agreement with the full Monte-Carlo simulation result for a wide range of system parameter space. These results could be of importance to the kinetic rates inference in Ribo-Seq data analysis and other related problems.

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Yahaya Ibrahim, Jérôme Dorignac, Fred Geniet, Carole Chevalier, Jean-Charles Walter, Nils-Ole Walliser, Andrea Pameggiani, John Palmeri. 2023-09-30. Chain decay and rates disorder in the totally asymmetric simple exclusion process. https://arxiv.org/abs/2310.00329

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