Exploring the mean-field and stochastic solutions for simple open TASEP-based models of ribosome translation

Abstract

The building blocks of life are underpinned by the central dogma of molecular biology, providing an explanation for the flow of genetic information towards protein synthesis. There has been a long standing discourse and vast literature of models proposing the mechanisms underlying the process of translation − in which the ribosomes decode RNA sequence into amino acids via degenerate triplet bases or codons. In this work, we explore the Totally Asymmetric Simple Exclusion Process (TASEP), developed in the framework of statistical mechanics, to model the translation mechanism as particle-hopping in a lattice or a "ribosome walk" across the mRNA sequence. We explore the mechanisms and dynamics of ribosomal RNA translation by building up from simplistic toy models towards more biologically relevant variants accounting for physiological and experimentally determined parameters.