Related papers: Power series method for solving TASEP-based models…
The totally asymmetric simple exclusion process (TASEP), which describes the stochastic dynamics of interacting particles on a lattice, has been actively studied over the past several decades and applied to model important biological…
We introduce a two-species exclusion model to describe the key features of the conflict between the RNA polymerase (RNAP) motor traffic, engaged in the transcription of a segment of DNA, concomitant with the progress of two DNA replication…
Motor protein motion on biopolymers can be described by models related to the totally asymmetric simple exclusion process (TASEP). Inspired by experiments on the motion of kinesin-4 motors on antiparallel microtubule overlaps, we analyze a…
Under certain cellular conditions, transcription and mRNA translation in prokaryotes appear to be "coupled," in which the formation of mRNA transcript and production of its associated protein are temporally correlated. Such…
The totally asymmetric simple exclusion principle (TASEP) is a fundamental model in nonequilibrium statistical mechanics. It describes the stochastic unidirectional movement of particles along a 1D chain of ordered sites. We consider the…
We investigate the totally asymmetric simple exclusion process (TASEP) in the presence of obstacles that dynamically bind and unbind from the lattice. The model is motivated by biological processes such as transcription in the presence of…
The totally asymmetric simple exclusion process (TASEP), a well-known model in its strictly one-dimensional (chain) version, is generalized to cylinder (nanotube) and ribbon (nanoribbon) geometries. A mean-field theoretical description is…
We present new results for the current as a function of transmission rate in the one dimensional totally asymmetric simple exclusion process (TASEP) with a blockage that lowers the jump rate at one site from one to r < 1. Exact finite…
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,…
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…
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…
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…
Transcription is a complex phenomenon that permits the conversion of genetic information into phenotype by means of an enzyme called RNA polymerase, which erratically moves along and scans the DNA template. We perform Bayesian inference…
The process of protein synthesis in biological systems resembles a one dimensional driven lattice gas in which the particles have spatial extent, covering more than one lattice site. We expand the well studied Totally Asymmetric Exclusion…
The asymmetric simple exclusion process (ASEP) is a model of particle transport used in the study of biological processes such as mRNA translation. In 2014, Zhao and Krishnan introduced a new approach for analyzing the ASEP using…
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…
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…
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…
Stochastic modeling of transcription is a classic yet long-standing problem in theoretical biophysics. The lack of unified results and a computationally efficient approach for a general, fine-grained transcription model has confined…
The totally asymmetric simple exclusion process (TASEP) is a basic model of statistical mechanics that has found numerous applications. We consider the case of TASEP with a finite chain where particles may enter from the left and leave to…