Related papers: Optimal Translation Along a Circular mRNA
Translation is an important stage in gene expression. During this stage, macro-molecules called ribosomes travel along the mRNA strand linking amino-acids together in a specific order to create a functioning protein. An important question…
Down regulation of mRNA translation is an important problem in various bio-medical domains ranging from developing effective medicines for tumors and for viral diseases to developing attenuated virus strains that can be used for…
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…
During mRNA translation, several ribosomes attach to the same mRNA molecule simultaneously translating it into a protein. This pipelining increases the protein production rate. A natural and important question is what ribosomal density…
Gene translation is the process in which intracellular macro-molecules, called ribosomes, decode genetic information in the mRNA chain into the corresponding proteins. Gene translation includes several steps. During the elongation step,…
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,…
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…
The ribosome flow model (RFM) is a phenomenological model for the unidirectional flow of particles along a 1D chain of $n$ sites. The RFM has been extensively used to study the dynamics of ribosome flow along a single mRNA molecule during…
The ribosomal density along the coding region of the mRNA molecule affect various fundamental intracellular phenomena including: protein production rates, organismal fitness, ribosomal drop off, and co-translational protein folding. Thus,…
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…
The Ribosome Flow Model (RFM) describes the unidirectional movement of interacting particles along a one-dimensional chain of sites. As a site becomes fuller, the effective entry rate into this site decreases. The RFM has been used to model…
We study a deterministic mechanistic model for the flow of ribosomes along the mRNA molecule, called the ribosome flow model with extended objects (RFMEO). This model encapsulates many realistic features of translation including…
The ribosome flow model (RFM) is a phenomenological model for the flow of particles along a 1D chain of $n$ sites. It has been extensively used to study ribosome flow along the mRNA molecule during translation. When the transition rates…
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…
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…
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…
We explore and quantify the physical and biochemical mechanisms that may be relevant in the regulation of translation. After elongation and detachment from the 3' termination site of mRNA, parts of the ribosome machinery can diffuse back to…
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…
Large-scale simultaneous mRNA translation and the resulting competition for the available ribosomes has important implications to the cell's functioning and evolution. Developing a better understanding of the intricate correlations between…