Modeling Translation in Protein Synthesis with TASEP: A Tutorial and Recent Developments

2011/04/12 by R. K. P. Zia, Jiajia Dong, J. J. Dong +1 · 214 citations
Biochemistry, Genetics and Molecular Biology · Mathematics · Physics and Astronomy · #Asymmetric simple exclusion process #Biology #Computer science #Gene #Gene Regulatory Network Analysis #Markov Chains and Monte Carlo Methods #Messenger RNA #Physics #Simple (philosophy) #Statistical physics #Stochastic processes and statistical mechanics #Translation (biology) #cond-mat.stat-mech #q-bio.QM

paper · pdf · doi:10.1007/s10955-011-0183-1

published in Journal of Statistical Physics 144(2), 405-428 (Springer Science+Business Media) · 25 pages, 7 figures

openalex publication_date 2011/04/12 · arxiv created 2011/08/16 · arxiv updated 2011/08/17 · openalex created_date 2025/10/10 · openalex updated_date 2026/08/05

Abstract

The phenomenon of protein synthesis has been modeled in terms of totally asymmetric simple exclusion processes (TASEP) since 1968. In this article, we provide a tutorial of the biological and mathematical aspects of this approach. We also summarize several new results, concerned with limited resources in the cell and simple estimates for the current (protein production rate) of a TASEP with inhomogeneous hopping rates, reflecting the characteristics of real genes.

Citations

• Boundary-induced phase transitions in traffic flow
• Inhomogeneous exclusion processes with extended objects: The effect of defect locations
• Local inhomogeneity in asymmetric simple exclusion processes with extended objects
• An exact solution of a one-dimensional asymmetric exclusion model with open boundaries
• Single-bottleneck approximation for driven lattice gases with disorder and open boundary conditions
• Bethe ansatz calculation of the spectral gap of the asymmetric exclusion process
• Central Dogma of Molecular Biology
• Asymmetric exclusion processes with disorder: Effect of correlations
• Time-dependent correlation functions in a one-dimensional asymmetric exclusion process
• Statistical Physics of Vehicular Traffic and Some Related Systems
• Ribosome Recycling, Diffusion, and mRNA Loop Formation in Translational Regulation
• Comparison of initiation of protein synthesis in procaryotes, eucaryotes, and organelles.

Cited by

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• Role of interactions in a closed quenched driven diffusive system
• Gene length as a regulator for ribosome recruitment and protein synthesis: theoretical insights.
• Negative feedback and oscillations in a model for mRNA translation