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On the Steady-State Distribution in the Homogeneous Ribosome Flow Model
Nov.-Dec. 2012 (vol. 9 no. 6)
pp. 1724-1736
| ASCII Text | x | ||
| M. Margaliot, T. Tuller, "On the Steady-State Distribution in the Homogeneous Ribosome Flow Model," IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 9, no. 6, pp. 1724-1736, Nov.-Dec., 2012. | |||
| BibTex | x | ||
| @article{ 10.1109/TCBB.2012.120, author = {M. Margaliot and T. Tuller}, title = {On the Steady-State Distribution in the Homogeneous Ribosome Flow Model}, journal ={IEEE/ACM Transactions on Computational Biology and Bioinformatics}, volume = {9}, number = {6}, issn = {1545-5963}, year = {2012}, pages = {1724-1736}, doi = {http://doi.ieeecomputersociety.org/10.1109/TCBB.2012.120}, publisher = {IEEE Computer Society}, address = {Los Alamitos, CA, USA}, } | |||
| RefWorks Procite/RefMan/Endnote | x | ||
| TY - JOUR JO - IEEE/ACM Transactions on Computational Biology and Bioinformatics TI - On the Steady-State Distribution in the Homogeneous Ribosome Flow Model IS - 6 SN - 1545-5963 SP1724 EP1736 EPD - 1724-1736 A1 - M. Margaliot, A1 - T. Tuller, PY - 2012 KW - physiological models KW - cellular biophysics KW - genetics KW - steady-state distribution KW - translation rate KW - ribosomal density profile KW - HRFM KW - mouse embryonic cells KW - coding sequence codons KW - computational model KW - gene translation KW - living organisms KW - biological process KW - homogeneous ribosome flow model KW - Computational modeling KW - Mathematical model KW - Biological system modeling KW - Bioinformatics KW - Steady-state KW - Encoding KW - constant elongation speed KW - Gene translation KW - systems biology KW - continued fractions KW - tridiagonal matrices KW - equilibrium point KW - monotone systems KW - translation elongation VL - 9 JA - IEEE/ACM Transactions on Computational Biology and Bioinformatics ER - | |||
DOI Bookmark: http://doi.ieeecomputersociety.org/10.1109/TCBB.2012.120
A central biological process in all living organisms is gene translation. Developing a deeper understanding of this complex process may have ramifications to almost every biomedical discipline. Reuveni et al. recently proposed a new computational model of gene translation called the Ribosome Flow Model (RFM). In this paper, we consider a particular case of this model, called the Homogeneous Ribosome Flow Model (HRFM). From a biological viewpoint, this corresponds to the case where the transition rates of all the coding sequence codons are identical. This regime has been suggested recently based on experiments in mouse embryonic cells. We consider the steady-state distribution of the HRFM. We provide formulas that relate the different parameters of the model in steady state. We prove the following properties: 1) the ribosomal density profile is monotonically decreasing along the coding sequence; 2) the ribosomal density at each codon monotonically increases with the initiation rate; and 3) for a constant initiation rate, the translation rate monotonically decreases with the length of the coding sequence. In addition, we analyze the translation rate of the HRFM at the limit of very high and very low initiation rate, and provide explicit formulas for the translation rate in these two cases. We discuss the relationship between these theoretical results and biological findings on the translation process.
Index Terms:
physiological models,cellular biophysics,genetics,steady-state distribution,translation rate,ribosomal density profile,HRFM,mouse embryonic cells,coding sequence codons,computational model,gene translation,living organisms,biological process,homogeneous ribosome flow model,Computational modeling,Mathematical model,Biological system modeling,Bioinformatics,Steady-state,Encoding,constant elongation speed,Gene translation,systems biology,continued fractions,tridiagonal matrices,equilibrium point,monotone systems,translation elongation
Citation:
M. Margaliot, T. Tuller, "On the Steady-State Distribution in the Homogeneous Ribosome Flow Model," IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 9, no. 6, pp. 1724-1736, Nov.-Dec. 2012, doi:10.1109/TCBB.2012.120
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