Related papers: Power series method for solving TASEP-based models…
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…
The Totally Asymmetric Simple Exclusion Process (TASEP) is an important example of a particle system driven by an irreversible Markov chain. In this paper we give a simple yet rigorous derivation of the chain stationary measure in the case…
We develope a theoretical framework, based on exclusion process, that is motivated by a biological phenomenon called transcript slippage (TS). In this model a discrete lattice represents a DNA strand while each of the particles that hop on…
We investigate the following question for machine translation (MT): can we develop a single universal MT model to serve as the common seed and obtain derivative and improved models on arbitrary language pairs? We propose mRASP, an approach…
Exclusion processes in one dimension first appeared in the 70s and have since dragged much attention from communities in different domains: stochastic processes, out-of-equilibriums statistical physics, and more recently integrable systems.…
The ribosome flow model (RFM) is a phenomenological model for the unidirectional flow of particles along a 1D chain of $n$ sites. The RFM has been extensively used to study the dynamics of ribosome flow along a single mRNA molecule during…
We introduce TASER (Translation Assessment via Systematic Evaluation and Reasoning), a metric that uses Large Reasoning Models (LRMs) for automated translation quality assessment. TASER harnesses the explicit reasoning capabilities of LRMs…
We study the totally asymmetric simple exclusion process (TASEP) on trees where particles are generated at the root. Particles can only jump away from the root, and they jump from $x$ to $y$ at rate $r_{x,y}$ provided $y$ is empty. Starting…
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 cascaded speech translation model relies on discrete and non-differentiable transcription, which provides a supervision signal from the source side and helps the transformation between source speech and target text. Such modeling suffers…
We investigate the totally asymmetric simple exclusion process (TASEP) in the presence of a bottleneck, i.e. a sequence of consecutive defect sites with reduced hopping rate. The influence of such a bottleneck on the phase diagram is…
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 introduce a family of layer to layer transfer matrices in a three-dimensional (3D) lattice model which can be viewed as partition functions of the $q$-oscillator valued six-vertex model on $m \times n$ square lattice. By invoking the…
We extend the paradigmatic and versatile TASEP (Totally Asymmetric Simple Exclusion Process) for stochastic 1d transport to allow for two different particle species, each having specific entry and exit rates. We offer a complete mean-field…
RNA polymerase (RNAP) is molecular machine that polymerizes a RNA molecule, a linear heteropolymer, using a single stranded DNA (ssDNA) as the corresponding template; the sequence of monomers of the RNA is dictated by that of monomers on…
Markov-chain Monte Carlo (MCMC), the field of stochastic algorithms built on the concept of sampling, has countless applications in science and technology. The overwhelming majority of MCMC algorithms are time-reversible and satisfy the…
Scanning Transmission Electron Microscopy (STEM) offers high-resolution images that are used to quantify the nanoscale atomic structure and composition of materials and biological specimens. In many cases, however, the resolution is limited…
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…
Protein translation is a multistep process which can be represented as a cascade of biochemical reactions (initiation, ribosome assembly, elongation, etc.), the rate of which can be regulated by small non-coding microRNAs through multiple…
Sampling from constrained distributions has a wide range of applications, including in Bayesian optimization and robotics. Prior work establishes convergence and feasibility guarantees for constrained sampling, but assumes that the feasible…