Related papers: Sensitivity of mRNA Translation
Relativistic beams of heavy ions interacting with various nuclear targets allow to study a broad range of problems starting from nuclear equation of state to the traditional nuclear structure. Some questions which were impossible to answer…
The totally asymmetric simple exclusion process with generalized update is a version of the discrete time totally asymmetric exclusion process with an additional inter-particle interaction that controls the degree of particle clustering.…
We develop a stochastic model for the programmed frameshift of ribosomes synthesizing a protein while moving along a mRNA template. Normally the reading frame of a ribosome decodes successive triplets of nucleotides on the mRNA in a…
We investigate theoretically the stochastic dynamics of Resonance Electronic Energy Transfer (RET), in a bi-dimensional overexcited ensemble of donor and acceptor molecules. We find that, after initial optical excitation of all the donors,…
The Totally Asymmetric Simple Exclusion Process (TASEP) is an important example of a particle system driven by an irreversible Markov chain. In this paper we give a simple yet rigorous derivation of the chain stationary measure in the case…
We consider an interacting particle system, which generalizes the classical totally asymmetric simple exclusion process (TASEP), in that each site can contain up to a fixed finite number of particles, and the particle movement is governed…
In this paper we consider the totally asymmetric simple exclusion process, with non-random initial condition having three regions of constant densities of particles. From left to right, the densities of the three regions are increasing.…
The time evolution of the thermally activated decay rates is considered. This evolution is of particular importance for the recent nanoscale experiments discussed in the literature, where the potential barrier is relatively low (or the…
The one-dimensional totally asymmetric simple exclusion process (TASEP) is considered. We study the time evolution property of a tagged particle in TASEP with the step-type initial condition. Calculated is the multi-time joint distribution…
We consider the partially asymmetric simple exclusion process (PASEP) when its steady-state probability distribution function can be written in terms of a linear superposition of product measures with a finite number of shocks. In this case…
Gene expression in individual cells is highly variable and sporadic, often resulting in the synthesis of mRNAs and proteins in bursts. Bursting in gene expression is known to impact cell-fate in diverse systems ranging from latency in HIV-1…
Using Monte Carlo simulations and a domain wall theory, we discuss the effect of coupling several totally asymmetric simple exclusion processes (TASEPs) to a finite reservoir of particles. This simple model mimics directed biological…
We study symmetric simple exclusion processes (SSEP) on a ring in the presence of uniformly moving multiple defects or disorders - a generalization of the model proposed earlier [Phys. Rev. E 89, 022138 (2014)]. The defects move with…
Detecting the translation direction of parallel text has applications for machine translation training and evaluation, but also has forensic applications such as resolving plagiarism or forgery allegations. In this work, we explore an…
We study an inhomogenous multispecies version of the Totally Asymmetric Simple Exclusion Process (TASEP) on a periodic oriented one dimensional lattice, which depends on two sets of parameters $({\bf \tau},{\bf \nu})$, attached to the…
We study asymmetric exclusion processes (TASEP) on a nonuniform one-dimensional ring consisting of two segments having unequal hopping rates, or {\em defects}. We allow weak particle nonconservation via Langmuir kinetics (LK), that are…
We introduce and analyze two general dynamical models for unidirectional movement of particles along a circular chain and an open chain of sites. The models include a soft version of the simple exclusion principle, that is, as the density…
The rapid advancements in transformer-based language models have revolutionized natural language processing, yet understanding the internal mechanisms of these models remains a significant challenge. This paper explores the application of…
Bidirectional transport in (quasi) one-dimensional systems generically leads to cluster-formation and small particle currents. This kind of transport can be described by the asymmetric simple exclusion process (ASEP) with two species of…
The one-dimensional totally asymmetric simple exclusion process (TASEP) with $N$ particles on a periodic lattice of $L$ sites is an interacting particle system with hopping rates breaking detailed balance. The total time-integrated current…