Related papers: Semi-Markov models of mRNA-translation
Translation is an important process for prokaryotic and eukaryotic cells to produce necessary proteins for cell growth. Numerious experiments have been performed to explore the translational properties. Diverse models have also been…
Translation is one of the main steps in the synthesis of proteins. It consists of ribosomes that translate sequences of nucleotides encoded on mRNA into polypeptide sequences of amino acids. Ribosomes bound to mRNA move unidirectionally,…
The process of polymerizing a protein by a ribosome, using a messenger RNA (mRNA) as the corresponding template, is called {\it translation}. Ribosome may be regarded as a molecular motor for which the mRNA template serves also as the…
Proteins are polymerized by cyclic machines called ribosome which use their messenger RNA (mRNA) track also as the corresponding template and the process is called translation. We explore, in depth and detail, the stochastic nature of the…
mRNA translation is a crucial process that leads to protein synthesis in living cells. Therefore, it is a process that needs to work optimally for a cell to stay healthy and alive. With advancements in microscopy and novel experimental…
Protein molecules in cells are synthesized by macromolecular machines called ribosomes. According to recent experimental data, we reduce the complexity of the ribosome and propose a model to express its activity in six main states. Using…
In the recent paper of Valleriani {\it et al} [Phys. Rev. E {\bf 83}, 042903 (2011)], a simple model for describing the translation of messenger RNA (mRNA) by ribosomes is presented, and an expression of the translational ratio $r$, defined…
Translation of mRNA into protein is a fundamental yet complex biological process with multiple factors that can potentially affect its efficiency. Here, we study a stochastic model describing the traffic flow of ribosomes along the mRNA…
The rate of mRNA translation depends on the initiation, elongation, and termination rates of ribosomes along the mRNA. These rates depend on many "local" factors like the abundance of free ribosomes and tRNA molecules in the vicinity of the…
Protein translation is one of the most important processes in cell life but, despite being well understood biochemically, the implications of its intrinsic stochastic nature have not been fully elucidated. In this paper we develop a…
The ribosome is one of the largest and most complex macromolecular machines in living cells. It polymerizes a protein in a step-by-step manner as directed by the corresponding nucleotide sequence on the template messenger RNA (mRNA) and…
The translation of messenger RNA transcripts to proteins is commonly modeled as a one-dimensional totally asymmetric exclusion process with extended particles. Here we focus on the effects of premature termination of translation through the…
Translation is a crucial step in gene expression. During translation, macromolecules called ribosomes "read" the mRNA strand in a sequential manner and produce a corresponding protein. Translation is known to consume most of the cell's…
Protein synthesis is one of the most fundamental biological processes, which consumes a significant amount of cellular resources. Despite existence of multiple mathematical models of translation, varying in the level of mechanistical…
Many {\it ribosomes} simultaneously move on the same messenger RNA (mRNA), each synthesizing separately a copy of the same protein. In contrast to the earlier models, here {\it we develop a ``unified'' theoretical model} that not only…
Messenger RNA translation is often studied by means of statistical-mechanical models based on the Asymmetric Simple Exclusion Process (ASEP), which considers hopping particles (the ribosomes) on a lattice (the polynucleotide chain). In this…
Recent advances in DNA sequencing and fluorescence imaging have made it possible to monitor the dynamics of ribosomes actively engaged in messenger RNA (mRNA) translation. Here, we model these experiments within the inhomogeneous totally…
Translation is a central biological process by which proteins are synthesized from genetic information contained within mRNAs. Here we study the kinetics of translation at molecular level through a stochastic simulation model. The model…
Many ribosomes simultaneously move on the same messenger RNA (mRNA), each separately synthesizing the protein coded by the mRNA. Earlier models of ribosome traffic represent each ribosome by a ``self-propelled particle'' and capture the…
We examine the dynamics of the translation stage of cellular protein production, in which ribosomes move uni-directionally along mRNA strands building an amino acid chain as they go. We describe the system using a timed event graph - a…