Related papers: Variability in mRNA Translation: A Random Matrix T…
Due to the stochastic nature of biochemical processes, the copy number of any given type of molecule inside a living cell often exhibits large temporal fluctuations. Here, we develop analytic methods to investigate how the noise arising…
Efficient protein synthesis depends on the availability of charged tRNA molecules. With 61 different codons, shifting the balance among the tRNA abundances can lead to large changes in the protein synthesis rate. Previous theoretical work…
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…
Diffusion models trained on different, non-overlapping subsets of a dataset often produce strikingly similar outputs when given the same noise seed. We trace this consistency to a simple linear effect: the shared Gaussian statistics across…
In $\textit{Escherichia coli}$ bacterium, the molecular compounds involved in protein synthesis, messenger RNAs (mRNAs) and ribosomes, show marked intracellular localization patterns. Yet a quantitative understanding of the physical…
The sequence of amino acid monomers in the primary structure of a protein is decided by the corresponding sequence of codons (triplets of nucleic acid monomers) on the template messenger RNA (mRNA). The polymerization of a protein, by…
Gene expression consists in the synthesis of proteins from the information encoded on DNA. One of the two main steps of gene expression is the translation of messenger RNA (mRNA) into polypeptide sequences of amino acids. Here, by taking…
The expression of genes usually follows a two-step procedure. First, a gene (encoded in the genome) is transcribed resulting in a strand of (messenger) RNA. Afterwards, the RNA is translated into protein. Classically, this gene expression…
Deprivation of essential nutrients can have stark consequences for many processes in a cell. We consider amino acid starvation, which can result in bottlenecks in mRNA translation when ribosomes stall due to lack of resources, i.e. tRNAs…
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…
Ribosome is a molecular machine that polymerizes a protein where the sequence of the amino acid residues, the monomers of the protein, is dictated by the sequence of codons (triplets of nucleotides) on a messenger RNA (mRNA) that serves as…
The eukaryotic protein synthesis process entails intricate stages governed by diverse mechanisms to tightly regulate translation. Translational regulation during stress is pivotal for maintaining cellular homeostasis, ensuring the accurate…
Proteins are polymers of amino acids. These macromolecules are synthesized by intracellular machines called ribosomes. Although the experimental investigation of protein synthesis has been a traditional area of research in molecular cell…
We analyse a simple discrete-time stochastic process for the theoretical modeling of the evolution of protein lengths. At every step of the process a new protein is produced as a modification of one of the proteins already existing and its…
Covariance matrices of amino acid displacements, commonly used to characterize the large-scale movements of proteins, are investigated through the prism of Random Matrix Theory. Bulk universality is detected in the local spacing statistics…
Recently discovered simple quantitative relations, known as bacterial growth laws, hint on the existence of simple underlying principles at the heart of bacterial growth. In this work, we provide a unifying picture on how these known…
Physiological changes which result in changes in bacterial gene expression are often accompanied by changes in the growth rate for fast adapting enteric bacteria. Since the availability of RNA polymerase (RNAP) in cells is dependent on the…
We develop a method for solving mathematical models of messenger RNA (mRNA) translation based on the totally asymmetric simple exclusion process (TASEP). Our main goal is to demonstrate that the method is versatile and applicable to…
The production processes of proteins in prokaryotic cells are investigated. Most of the mathematical models in the literature study the production of {\em one} fixed type of proteins. When several classes of proteins are considered, an…
We study a stochastic model of gene expression, in which protein production has a form of random bursts whose size distribution is arbitrary, whereas protein decay is a first-order reaction. We find exact analytical expressions for the time…