Related papers: Sensitivity of mRNA Translation
Experimental evidences show that in gene transcription, RNA polymerase has the possibility to be stalled at certain position of the transcription template. This may be due to the template damage, or protein barriers. Once stalled,…
In this paper we analyze the equilibrium properties of a large class of stochastic processes describing the fundamental biological process within bacterial cells, {\em the production process of proteins}. Stochastic models classically used…
We study the totally asymmetric simple exclusion process (TASEP) on trees where particles are generated at the root. Particles can only jump away from the root, and they jump from $x$ to $y$ at rate $r_{x,y}$ provided $y$ is empty. Starting…
We introduce a biologically detailed, stochastic model of gene expression describing the multiple rate-limiting steps of transcription, nuclear pre-mRNA processing, nuclear mRNA export, cytoplasmic mRNA degradation and translation of mRNA…
MicroRNAs can affect the protein translation using nine mechanistically different mechanisms, including repression of initiation and degradation of the transcript. There is a hot debate in the current literature about which mechanism and in…
Cells use genetic switches to shift between alternate gene expression states, e.g., to adapt to new environments or to follow a developmental pathway. Here, we study the dynamics of switching in a generic-feedback on/off switch. Unlike…
In a previous study we developed a mean-field theory of dynamical transitions for the totally-asymmetric simple-exclusion process (TASEP) with open boundaries and Langmuir kinetics, in the so-called balanced regime, characterized by equal…
Tight regulation of messenger RNA (mRNA) stability is essential to ensure accurate gene expression in response to developmental and environmental cues. mRNA stability is controlled by mRNA decay pathways, which have traditionally been…
We consider steady-state current activity statistics for the one-dimensional totally asymmetric simple exclusion process (TASEP). With the help of the known operator algebra (for general open boundary conditions), as well as general…
Motivated by recent experiments on an antibiotic resistance gene, we investigate genetic interactions between synonymous mutations in the framework of exclusion models of translation. We show that the range of possible interactions is…
We explore how the interplay of finite availability, carrying capacity of particles at different parts of a spatially extended system and particle diffusion between them control the steady state currents and density profiles in a…
Smooth transportation has drawn the attention of many researchers and practitioners in several fields. In the present paper, we propose a modified model of a totally asymmetric simple exclusion process (TASEP), which includes multiple…
We describe the translation invariant stationary states of the one dimensional discrete-time facilitated totally asymmetric simple exclusion process (F-TASEP). In this system a particle at site $j$ in $Z$ jumps, at integer times, to site…
During cellular translation, incorporation errors occur. It is the addition of amino acid residues not corresponding to the mRNA code. With an increase in the number of residues in the synthesized molecule, the probability of failure in at…
Stochasticity in gene expression gives rise to fluctuations in protein levels across a population of genetically identical cells. Such fluctuations can lead to phenotypic variation in clonal populations, hence there is considerable interest…
Heritable differences in gene expression between individuals are an important source of phenotypic variation. The question of how closely the effects of genetic variation on protein levels mirror those on mRNA levels remains open. Here, we…
Individual mRNAs are translated by multiple ribosomes that initiate translation with a few seconds interval. The ribosome speed is codon dependant, and ribosome queuing has been suggested to explain specific data for translation of some…
We discuss a general mean field plus random phase approximation (RPA) for describing composite systems at zero and finite temperature. We analyze in particular its implementation in finite systems invariant under translations, where for…
Several theoretical models based on totally asymmetric simple exclusion process (TASEP) have been extensively utilized to study various non-equilibrium transport phenomena. Inspired by the the role of microtubule-transported vesicles in…
We revisit the totally asymmetric simple exclusion process with open boundaries (TASEP), focussing on the recent discovery by de Gier and Essler that the model has a dynamical transition along a nontrivial line in the phase diagram. This…