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Translation is an important process for prokaryotic and eukaryotic cells to produce necessary proteins for cell growth. Numerious experiments have been performed to explore the translational properties. Diverse models have also been…

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…

Inferring unknown initial states in shock-dominated compressible flows from sparse and noisy measurements is a challenging ill-posed inverse problem due to nonlinear wave interactions and limited sensing. In this work, we develop a…

We explore and quantify the physical and biochemical mechanisms that may be relevant in the regulation of translation. After elongation and detachment from the 3' termination site of mRNA, parts of the ribosome machinery can diffuse back to…

The Totally Asymmetric Simple Exclusion Process (TASEP) is a paradigm of out-of-equilibrium Statistical Physics that serves as a simplistic model for one-way vehicular traffic. Since traffic is perturbed by cars cruising for parking in many…

A novel machine learning algorithm is presented, serving as a data-driven turbulence modeling tool for Reynolds Averaged Navier-Stokes (RANS) simulations. This machine learning algorithm, called the Tensor Basis Random Forest (TBRF), is…

We address how the interplay between the finite availability and carrying capacity of particles at different parts of a spatially extended system can control the steady state currents and density profiles in the one-dimensional…

The ribosomal density along the coding region of the mRNA molecule affect various fundamental intracellular phenomena including: protein production rates, organismal fitness, ribosomal drop off, and co-translational protein folding. Thus,…

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…

We introduce a new model to study the oscillations of opposite flows sharing a common bottleneck and moving on two Totally Asymmetric Simple Exclusion Process (TASEP) lanes. We provide a theoretical analysis of the phase diagram, valid when…

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…

We consider the one-dimensional totally asymmetric simple exclusion process (TASEP) with position-dependent hopping rates. The problem is solved,in a mean field/adiabatic approximation, for a general (smooth) form of spatial rate variation.…

Reduced order models (ROMs) play a critical role in fluid mechanics by providing low-cost predictions, making them an attractive tool for engineering applications. However, for ROMs to be widely applicable, they must not only generalise…

We describe the translation invariant stationary states of the one dimensional discrete-time facilitated totally asymmetric simple exclusion process (F-TASEP). In this system a particle at site $j$ in $Z$ jumps, at integer times, to site…

The TASEP is a paradigmatic model from non-equilibrium statistical physics, which describes particles hopping along a lattice of discrete sites. The TASEP is applicable to a broad range of different transport systems, but does not consider…

The totally asymmetric simple exclusion process (TASEP) is a paradigmatic stochastic model for non-equilibrium physics, and has been successfully applied to describe active transport of molecular motors along cytoskeletal filaments.…

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 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 revisit the defect-induced nonequilibrium phase transition from a largely homogeneous free-flow phase to a phase-separated congested phase in the sublattice totally asymmetric simple exclusion process (TASEP) with local deterministic…

Using the dynamic mean-field approximation of the totally asymmetric simple exclusion process (TASEP), we investigate the effect of small changes in the initiation, exit, and elongation rates along the mRNA strand on the steady state…