Related papers: Modeling Translation in Protein Synthesis with TAS…
We develop a mean-field theory for the totally asymmetric simple exclusion process (TASEP) with open boundaries, in order to investigate the so-called dynamical transition. The latter phenomenon appears as a singularity in the relaxation…
The translation of messenger RNA transcripts to proteins is commonly modeled as a one-dimensional totally asymmetric exclusion process with extended particles. Here we focus on the effects of premature termination of translation through the…
Introduced in the late 1960's, the asymmetric exclusion process (ASEP) is an important model from statistical mechanics which describes a system of interacting particles hopping left and right on a one-dimensional lattice of n sites with…
We study the totally asymmetric simple exclusion process (TASEP) on $\mathbb{Z}$ with step initial condition, in which all particles have distinct types. Our main object of interest is the type of the rightmost particle -- the leader -- at…
Theoretical advances in the study of non-equilibrium phenomena are briefly reviewed with emphasis on steady state properties of one-dimensional driven lattice gases. The presentation is focused on the totally asymmetric simple-exclusion…
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 introduce an $n$-species totally asymmetric zero range process ($n$-TAZRP) on one-dimensional periodic lattice with $L$ sites. It is a continuous time Markov process in which $n$ species of particles hop to the adjacent site only in one…
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.…
The theory of biochemical processes needs simple but realistic models of phenomena underlying microscopic dynamics of proteins. Many experiments performed in the 1980s have demonstrated that within the protein native state, apart from usual…
We introduce a mean-field theoretical framework to describe multiple totally asymmetric simple exclusion processes (TASEPs) with different lattice lengths, entry and exit rates, competing for a finite reservoir of particles. We present…
Generalization of the one-dimensional totally asymmetric exclusion process (TASEP) with open boundary conditions in which particles are allowed to jump $l$ sites ahead with the probability $p_l\sim 1/l^{\sigma+1}$ is studied by Monte Carlo…
Totally Asymmetric Simple Exclusion Process (TASEP) on $\mathbb{Z}$ is one of the classical exactly solvable models in the KPZ universality class. We study the "slow bond" model, where TASEP on $\mathbb{Z}$ is imputed with a slow bond at…
Translation is the cellular process in which ribosomes make proteins from information encoded on messenger RNA (mRNA). We model translation with an exclusion process taking into account the experimentally determined, non-exponential,…
Molecular Dynamics (MD) simulations are fundamental computational tools for the study of proteins and their free energy landscapes. However, sampling protein conformational changes through MD simulations is challenging due to the relatively…
We consider the totally asymmetric simple exclusion process (TASEP) starting with a shock discontinuity at the origin, with asymptotic densities $\lambda$ to the left of the origin and $\rho$ to the right of it and $\lambda<\rho$. We find…
We investigate a balance network of the asymmetric simple exclusion process (ASEP). Subsystems consisting of ASEPs are connected by bidirectional links with each other, which results in balance between every pair of subsystems. The network…
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…
Prediction of protein structures using computational approaches has been explored for over two decades, paving a way for more focused research and development of algorithms in comparative modelling, ab intio modelling and structure…
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 study combinatorial structures arising from finite-time transition probabilities of the Totally Asymmetric Simple Exclusion Process with open boundary conditions. While much of the existing combinatorial theory regarding the TASEP…