Related papers: Modeling Translation in Protein Synthesis with TAS…
We study an inhomogenous multispecies version of the Totally Asymmetric Simple Exclusion Process (TASEP) on a periodic oriented one dimensional lattice, which depends on two sets of parameters $({\bf \tau},{\bf \nu})$, attached to the…
We derive exact solutions of simplified models for the temporal evolution of the protein concentration within a cell population arbitrarily far from the stationary state. We show that monitoring the dynamics can assist in modeling and…
Protein structure prediction and folding are fundamental to understanding biology, with recent deep learning advances reshaping the field. Diffusion-based generative models have revolutionized protein design, enabling the creation of novel…
Cellular functions are established through biological evolution, but are constrained by the laws of physics. For instance, the physics of protein folding limits the lengths of cellular polypeptide chains. Consequently, many cellular…
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 construct an algorithm that generates large, band-diagonal transition matrices for a totally asymmetric exclusion process (TASEP) with local hopping rate inhomogeneities. The matrices are diagonalized numerically to find steady-state…
In this paper, we consider zero range process with an initial condition which is equivalent to step initial condition in total asymmetric simple exclusion process (TASEP) as described in a paper by R\'akos, A. and Sch\"utz by using…
We study the totally asymmetric exclusion process (TASEP) on a finite one-dimensional lattice with open boundaries, i.e., in contact with two reservoirs at different potentials. The total (time-integrated) current through the system is a…
A totally asymmetric exclusion process on a ring with $\nu$ non-conserved internal degrees of freedom, where particles hop forward with a rate that depends on their internal state, has been studied. We show, using a mapping of the model to…
Proteins are macromolecules that mediate a significant fraction of the cellular processes that underlie life. An important task in bioengineering is designing proteins with specific 3D structures and chemical properties which enable…
The one-dimensional asymmetric simple exclusion process (ASEP), where $N$ hard-core particles hop forward with rate $1$ and backward with rate $q<1$, is considered on a periodic lattice of $L$ site. Using KPZ universality and previous…
This is an expanded version of a series of lectures delivered by the second author in June, 2009. It describes the results of three of the authors' papers on ASEP, from the derivation of exact formulas for configuration probabilities,…
In this paper we consider the totally asymmetric simple exclusion process, with non-random initial condition having three regions of constant densities of particles. From left to right, the densities of the three regions are increasing.…
The asymmetric simple exclusion process (ASEP) is a paradigmatic driven-diffusive system that describes the asymmetric diffusion of particles with hardcore interactions in a lattice. Although the ASEP is known as an exactly solvable model,…
We construct a one-dimensional totally asymmetric simple exclusion process (TASEP) on a ring with two segments having unequal hopping rates, coupled to particle non-conserving Langmuir kinetics (LK) characterized by equal attachment and…
The totally asymmetric exclusion process (TASEP) with periodic boundaries is considered as traffic flow model. The large-L approximation of the stationary state is used for the derivation of the time-headway distribution (an important…
We study the steady state of the two-species Asymmetric Simple Exclusion Process (ASEP) with open boundary conditions. The matrix product method works for the determination of the stationary probability distribution. Several physical…
We introduce the multispecies totally asymmetric simple exclusion process (mTASEP) with long-range swap, a new interacting particle system combining the backward-push rule with the forward-jump rule. Although governed by local dynamics, the…
Rapid progress in deep learning has spurred its application to bioinformatics problems including protein structure prediction and design. In classic machine learning problems like computer vision, progress has been driven by standardized…
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…