Related papers: Sensitivity of mRNA Translation
In many important cellular processes, including mRNA translation, gene transcription, phosphotransfer, and intracellular transport, biological "particles" move along some kind of "tracks". The motion of these particles can be modeled as a…
We prove an exact solution of a multi-lane totally asymmetric simple exclusion process (TASEP) with heterogeneous lane-changing rates on a torus. The solution is given by a factorized form; that is, the TASEP in each lane and lane-changing…
Network translation has recently been used to establish steady state properties of mass action systems by corresponding the given system to a generalized one which is either dynamically or steady state equivalent. In this work we further…
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…
Current fluctuations for the one-dimensional totally asymmetric exclusion process (TASEP) connected to reservoirs of particles, and their large scale limit to the KPZ fixed point in finite volume, are studied using exact methods. Focusing…
The transfer matrix and matrix multiplication ansatz, when applied to nonequilibrium steady states in asymmetric exclusion processed and traffic models, has given many exact results for phase diagrams, bulk densities and fluxes, as well as…
A simple stochastic model of a self regulating gene that displays bistable switching is analyzed. While on, a gene transcribes mRNA at a constant rate. Transcription factors can bind to the DNA and affect the gene's transcription rate.…
We apply the Matrix Product Ansatz to study the Totally Asymmetric Simple Exclusion Process on a ring with a generalized discrete-time dynamics depending on two hopping probabilities, $p$ and $\tilde{p}$. The model contains as special cases…
We introduce a class of distance-dependent interactions in an accelerated exclusion process (AEP) inspired by the observation of transcribing RNA polymerase speeding up when "pushed" by a trailing one. On a ring, the AEP steady state…
Gene expression is significantly stochastic making modeling of genetic networks challenging. We present an approximation that allows the calculation of not only the mean and variance but also the distribution of protein numbers. We assume…
The totally asymmetric simple exclusion process (TASEP) on Z with the Bernoulli-rho measure as initial conditions, 0<rho<1, is stationary. It is known that along the characteristic line, the current fluctuates as of order t^{1/3}. The…
We discuss the approximate phenomenological description of the motion of a single second-class particle in a two-species totally asymmetric simple exclusion process (TASEP) on a 1D lattice. Initially, the second class particle is located at…
We investigate the totally asymmetric simple exclusion process on closed and directed random regular networks, which is a simple model of active transport in the one-dimensional segments coupled by junctions. By a pair mean-field theory and…
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…
The asymmetric simple exclusion process (ASEP) is a fundamental stochastic model describing asymmetric many-particle diffusion with hard-core interactions on a one-dimensional lattice, and has been widely applied in the study of…
A system consisting of two parallel coupled channels where particles in one of them follow the rules of totally asymmetric exclusion processes (TASEP) and in another one move as in symmetric simple exclusion processes (SSEP) is investigated…
We derive a formula for the quasi-potential of one-dimensional symmetric exclusion process in weak contact with reservoirs. The interaction with the boundary is so weak that, in the diffusive scale, the density profile evolves as the one of…
We consider the totally asymmetric simple exclusion process (TASEP) on a periodic one-dimensional lattice of L sites. Using Bethe ansatz, we derive parametric formulas for the eigenvalues of its generator in the thermodynamic limit. This…
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…
The folding dynamics of small single-domain proteins is a current focus of simulations and experiments. Many of these proteins are 'two-state folders', i.e. proteins that fold rather directly from the denatured state to the native state,…