Related papers: Sensitivity of mRNA Translation
The asymmetric simple exclusion process (ASEP) is an important model from statistical physics describing particles that hop randomly from one site to the next along an ordered lattice of sites, but only if the next site is empty. ASEP has…
In cells, most of cargos are transported by motor proteins along microtubule. Biophysically, unidirectional motion of large number of motor proteins along a single track can be described by totally asymmetric simple exclusion process…
A discrete-time totally asymmetric simple exclusion process on a lattice with open boundaries is considered. There are particles of different types. The type of a particle is characterized by the probability that a particle moves to a…
We study a totally asymmetric simple exclusion process (TASEP) with one defect site, hopping rate $q<1$, near the system boundary. Regarding our system as a pair of uniform TASEP's coupled through the defect, we study various methods to…
In this article we present a comprehensive study of the totally asymmetric simple exclusion process with pausing particles (pTASEP), a model initially introduced to describe RNAP dynamics during transcription. We extend previous mean-field…
One of the greatest challenges in biophysical models of translation is to identify coding sequences features that affect the rate of translation and therefore the overall protein production in the cell. We propose an analytic method to…
A theory for qualitative models of gene regulatory networks has been developed over several decades, generally considering transcription factors to regulate directly the expression of other transcription factors, without any intermediate…
In a recent study [C Arita, Phys. Rev. E 80, 051119 (2009)], an extension of the M/M/1 queueing process with the excluded-volume effect as in the totally asymmetric simple exclusion process (TASEP) was introduced. In this paper, we consider…
We investigate the stationary distribution of asymmetric and weakly asymmetric simple exclusion processes with open boundaries. We project the stationary distribution onto a subinterval, whose size is allowed to grow with the length of the…
We study the effects of local inhomogeneities, i.e., slow sites of hopping rate $q<1$, in a totally asymmetric simple exclusion process (TASEP) for particles of size $\ell \geq 1$ (in units of the lattice spacing). We compare the simulation…
Proteins are polymerized by cyclic machines called ribosome which use their messenger RNA (mRNA) track also as the corresponding template and the process is called translation. We explore, in depth and detail, the stochastic nature of the…
Protein molecules in cells are synthesized by macromolecular machines called ribosomes. According to recent experimental data, we reduce the complexity of the ribosome and propose a model to express its activity in six main states. Using…
We explore the stationary densities in totally asymmetric exclusion processes (TASEP) with open boundary conditions and spatially inhomogeneous hopping rates. We calculate the steady state density profiles that characterise the associated…
In the multi-type totally asymmetric simple exclusion process (TASEP) on the line, each site of Z is occupied by a particle labeled with some number, and two neighboring particles are interchanged at rate one if their labels are in…
Intrinsic transcriptional noise induced by operator fluctuations is investigated with a simple spin like stochastic model. The effects of transcriptional fluctuations in protein synthesis is probed by coupling transcription and translation…
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 totally asymmetric simple exclusion process in discrete time is considered on finite rings with fixed number of particles. A translation-invariant version of the backward-ordered sequential update is defined for periodic boundary…
The totally asymmetric simple exclusion process (TASEP) is a stochastic model for the unidirectional flow of interacting particles on a 1D-lattice that is much used in systems biology and statistical physics. Its master equation describes…
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…
For the canonical two-state model of transcription, we derive exact analytic expressions for the entropy production rate of transcription at steady state, and assess detailed balance breaking in transcription. Our analytics allow us to…