Totally Asymmetric Exclusion Process Research Articles

Nonequilibrium steady states in coupled asymmetric and symmetric exclusion processes.

We propose and study a one-dimensional (1D) model consisting of two lanes with open boundaries. One of the lanes executes diffusive and the other lane driven unidirectional or asymmetric exclusion dynamics, which are mutually coupled through particle exchanges in the bulk. We elucidate the generic nonuniform steady states in this model. We show that in a parameter regime, where hopping along the TASEP lane, diffusion along the SEP lane, and the exchange of particles between the TASEP and SEP lanes compete, the SEP diffusivity D appears as a tuning parameter for both the SEP and TASEP densities for a given exchange rate in the nonequilibrium steady states of this model. Indeed, D can be tuned to achieve phase coexistence in the asymmetric exclusion dynamics together with spatially smoothly varying density in the diffusive dynamics in the steady state. We obtain phase diagrams of the model using mean field theories, and corroborate and complement the results with stochastic Monte Carlo simulations. This model reduces to an isolated open totally asymmetric exclusion process (TASEP) and an open TASEP with bulk particle nonconserving Langmuir kinetics (LK), respectively, in the limits of vanishing and diverging particle diffusivity in the lane executing diffusive dynamics. Thus, this model works as an overarching general model, connecting both pure TASEPs and TASEPs with LK in different asymptotic limits. We further define phases in the SEP and obtain phase diagrams and show their correspondence with the TASEP phases. In addition to its significance as a 1D driven, diffusive model, this model also serves as a simple reduced model for cell biological transport by molecular motors undergoing diffusive and directed motion inside eukaryotic cells.

Steady states and phase transitions in heterogeneous asymmetric exclusion processes

We study nonequilibrium steady states in totally asymmetric exclusion processes (TASEPs) with open boundary conditions having spatially inhomogeneous hopping rates. Considering smoothly varying hopping rates, we show that the steady states are in general classified by the steady state currents in direct analogy with open TASEPs having uniform hopping rates. We calculate the steady state bulk density profiles, which are now spatially nonuniform. We also obtain the phase diagrams in the plane of the control parameters, which, despite having phase boundaries that are in general curved lines, have the same topology as their counterparts for conventional open TASEPs, independent of the form of the hopping rate functions. This reveals a type of universality, not encountered in critical phenomena. Surprisingly and in contrast to the phase transitions in an open TASEP with uniform hopping, our studies on the phase transitions in the model reveal that all three transitions are first order in nature. We also demonstrate that this model admits delocalised domain walls (DDWs) on the phase boundaries, demarcating the generalised low and high density phases in this model. However, in contrast to the DDWs observed in an open TASEP with uniform hopping, the envelopes of the DDWs in the present model are generally curved lines.

Traffic modeling on the road of the fly over branch using totally asymmetric exclusion process a macroscopic approach

This research examines a dynamic model, namely the Totally Asymmetric Exclusion Process (TASEP). In addition, it discusses the boundary conditions and dynamic rules used in this modeling. TASEP has been applied in various fields, one of which is the traffic flow modeling. This system is modified into a unidirectional fly-over fork. Furthermore, a vehicle which travels through a road segment is modeled as a particle which jumps from one lattice to another. The continuity term which is to describe a particle dynamic in TASEP is solved by using the level set method. The profile of particle density and current density is affected by input rate and output rate of the particle jump.

Investigation of attractive interactions in a self-driven unidirectional two-channel model with periodic and open boundaries

The totally asymmetric exclusion process (TASEP) is an outstanding paradigm of self-driven particle models. A new two-channel TASEP model with short-range interactions in horizontal and vertical directions is given. The dynamic properties of the system with periodic boundary and open boundary are investigated by computer simulation and theoretical analysis. The analysis results based on the cluster mean-field method agree very well with the simulations. The flow rate of the system decreases for the strong attractive interaction, and the high-density phase region in the phase diagram extends accordingly.

Pinned or moving: States of a single shock in a ring.

Totally asymmetric exclusion processes (TASEPs) with open boundaries are known to exhibit moving shocks or delocalized domain walls (DDWs) for sufficiently small equal injection and extraction rates. In contrast, TASEPs in a ring with a single inhomogeneity display pinned shocks or localized domain walls (LDWs) under equivalent conditions [see, e.g., H. Hinsch and E. Frey, Phys. Rev. Lett. 97, 095701 (2006)PRLTAO0031-900710.1103/PhysRevLett.97.095701]. By studying periodic exclusion processes composed of a driven (TASEP) and a diffusive segment, we discuss gradual fluctuation-induced depinning of the LDW, leading to its delocalization and formation of a DDW-like domain wall, similar to the DDWs in open TASEPs in some limiting cases under long-time averaging. This smooth crossover is controlled essentially by the fluctuations in the diffusive segment. Our studies provide an explicit route to control the quantitative extent of domain-wall fluctuations in driven periodic inhomogeneous systems, and should be relevant in any quasi-one-dimensional transport processes where the availability of carriers is the rate-limiting constraint.

Transverse temperature interfaces in the Katz-Lebowitz-Spohn driven lattice gas.

We explore the intriguing spatial patterns that emerge in a two-dimensional spatially inhomogeneous Katz-Lebowitz-Spohn (KLS) driven lattice gas with attractive nearest-neighbor interactions. The domain is split into two regions with hopping rates governed by different temperatures T>T_{c} and T_{c}, respectively, where T_{c} indicates the critical temperature for phase ordering, and with the temperature boundaries oriented perpendicular to the drive. In the hotter region, the system behaves like the (totally) asymmetric exclusion processes (TASEP), and experiences particle blockage in front of the interface to the critical region. To explain this particle density accumulation near the interface, we have measured the steady-state current in the KLS model at T>T_{c} and found it to decay as 1/T. In analogy with TASEP systems containing "slow" bonds, we argue that transport in the high-temperature subsystem is impeded by the lower current in the cooler region, which tends to set the global stationary particle current value. This blockage is induced by the extended particle clusters, growing logarithmically with system size, in the critical region. We observe the density profiles in both high- and low-temperature subsystems to be similar to the well-characterized coexistence and maximal-current phases in (T)ASEP models with open boundary conditions, which are respectively governed by hyperbolic and trigonometric tangent functions. Yet if the lower temperature is set to T_{c}, we detect marked fluctuation corrections to the mean-field density profiles, e.g., the corresponding critical KLS power-law density decay near the interfaces into the cooler region.

Rényi entropy of the totally asymmetric exclusion process

The Rényi entropy is a generalisation of the Shannon entropy that is sensitive to the fine details of a probability distribution. We present results for the Rényi entropy of the totally asymmetric exclusion process (TASEP). We calculate explicitly an entropy whereby the squares of configuration probabilities are summed, using the matrix product formalism to map the problem to one involving a six direction lattice walk in the upper quarter plane. We derive the generating function across the whole phase diagram, using an obstinate kernel method. This gives the leading behaviour of the Rényi entropy and corrections in all phases of the TASEP. The leading behaviour is given by the result for a Bernoulli measure and we conjecture that this holds for all Rényi entropies. Within the maximal current phase the correction to the leading behaviour is logarithmic in the system size. Finally, we remark upon a special property of equilibrium systems whereby discontinuities in the Rényi entropy arise away from phase transitions, which we refer to as secondary transitions. We find no such secondary transition for this nonequilibrium system, supporting the notion that these are specific to equilibrium cases.

TASEP of interacting particles of arbitrary size

A mean-field description of the stationary state behaviour of interacting k-mers performing totally asymmetric exclusion processes (TASEP) on an open lattice segment is presented employing the discrete Takahashi formalism. It is shown how the maximal current and the phase diagram, including triple-points, depend on the strength of repulsive and attractive interactions. We compare the mean-field results with Monte Carlo simulation of three types interacting k-mers: monomers, dimers and trimers. (a) We find that the Takahashi estimates of the maximal current agree quantitatively with those of the Monte Carlo simulation in the absence of interaction as well as in both the the attractive and the strongly repulsive regimes. However, theory and Monte Carlo results disagree in the range of weak repulsion, where the Takahashi estimates of the maximal current show a monotonic behaviour, whereas the Monte Carlo data show a peaking behaviour. It is argued that the peaking of the maximal current is due to a correlated motion of the particles. In the limit of very strong repulsion the theory predicts a universal behavior: th maximal currents of k-mers correspond to that of non-interacting -mers; (b) Monte Carlo estimates of the triple-points for monomers, dimers and trimers show an interesting general behaviour : (i) the phase boundaries and for entry and exit current, respectively, as function of interaction strengths show maxima for whereas exhibit minima at the same strength; (ii) in the attractive regime, however, the trend is reversed (). The Takahashi estimates of the triple-point for monomers show a similar trend as the Monte Carlo data except for the peaking of ; for dimers and trimers, however, the Takahashi estimates show an opposite trend as compared to the Monte Carlo data.

Braess paradox in a network of totally asymmetric exclusion processes.

We study the Braess paradox in the transport network as originally proposed by Braess with totally asymmetric exclusion processes (TASEPs) on the edges. The Braess paradox describes the counterintuitive situation in which adding an edge to a road network leads to a user optimum with higher travel times for all network users. Travel times on the TASEPs are nonlinear in the density, and jammed states can occur due to the microscopic exclusion principle, leading to a more realistic description of trafficlike transport on the network than in previously studied linear macroscopic mathematical models. Furthermore, the stochastic dynamics allows us to explore the effects of fluctuations on network performance. We observe that for low densities, the added edge leads to lower travel times. For slightly higher densities, the Braess paradox occurs in its classical sense. At intermediate densities, strong fluctuations in the travel times dominate the system's behavior due to links that are in a domain-wall state. At high densities, the added link leads to lower travel times. We present a phase diagram that predicts the system's state depending on the global density and crucial path-length ratios.

Time-headway distribution for periodic totally asymmetric exclusion process with various updates

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 microscopic characteristic of traffic flow) for the model with generalized update (genTASEP) in both, forward- and backward-sequential representations. The usually used updates, fully-parallel and regular forward- and backward-sequential, are analyzed as special cases of the genTASEP. It is shown that only for those cases, the time-headway distribution is determined by the flow regardless to the density. The qualitative comparison of the results with traffic data demonstrates that the genTASEP with backward order and attractive interaction evinces similar properties of time-headway distribution as the real traffic sample.

On-site residence time in a driven diffusive system: Violation and recovery of a mean-field description.

We investigate simple one-dimensional driven diffusive systems with open boundaries. We are interested in the average on-site residence time defined as the time a particle spends on a given site before moving on to the next site. Using mean-field theory, we obtain an analytical expression for the on-site residence times. By comparing the analytic predictions with numerics, we demonstrate that the mean-field significantly underestimates the residence time due to the neglect of time correlations in the local density of particles. The temporal correlations are particularly long-lived near the average shock position, where the density changes abruptly from low to high. By using domain wall theory, we obtain highly accurate estimates of the residence time for different boundary conditions. We apply our analytical approach to residence times in a totally asymmetric exclusion process (TASEP), TASEP coupled to Langmuir kinetics (TASEP+LK), and TASEP coupled to mutually interactive LK (TASEP+MILK). The high accuracy of our predictions is verified by comparing these with detailed Monte Carlo simulations.

Unbiased Quantitative Models of Protein Translation Derived from Ribosome Profiling Data.

Translation of RNA to protein is a core process for any living organism. While for some steps of this process the effect on protein production is understood, a holistic understanding of translation still remains elusive. In silico modelling is a promising approach for elucidating the process of protein synthesis. Although a number of computational models of the process have been proposed, their application is limited by the assumptions they make. Ribosome profiling (RP), a relatively new sequencing-based technique capable of recording snapshots of the locations of actively translating ribosomes, is a promising source of information for deriving unbiased data-driven translation models. However, quantitative analysis of RP data is challenging due to high measurement variance and the inability to discriminate between the number of ribosomes measured on a gene and their speed of translation. We propose a solution in the form of a novel multi-scale interpretation of RP data that allows for deriving models with translation dynamics extracted from the snapshots. We demonstrate the usefulness of this approach by simultaneously determining for the first time per-codon translation elongation and per-gene translation initiation rates of Saccharomyces cerevisiae from RP data for two versions of the Totally Asymmetric Exclusion Process (TASEP) model of translation. We do this in an unbiased fashion, by fitting the models using only RP data with a novel optimization scheme based on Monte Carlo simulation to keep the problem tractable. The fitted models match the data significantly better than existing models and their predictions show better agreement with several independent protein abundance datasets than existing models. Results additionally indicate that the tRNA pool adaptation hypothesis is incomplete, with evidence suggesting that tRNA post-transcriptional modifications and codon context may play a role in determining codon elongation rates.

Defect-induced phase transition in the asymmetric simple exclusion process

We reconsider the long-standing question of the critical defect hopping rate rc in the one-dimensional totally asymmetric exclusion process (TASEP) with a slow bond (defect). For r < rc a phase-separated state is observed due to queuing at the defect site, whereas for the defect site, has only local effects on the stationary state of the homogeneous system. Mean-field theory predicts (when hopping rates outside the defect bond are equal to 1) but numerical investigations seem to indicate . Here we improve the numerics to show that rc > 0.99 and give strong evidence that indeed as predicted by mean-field theory, and anticipated by recent theoretical findings.

Emergence of jams in the generalized totally asymmetric simple exclusion process.

The generalized totally asymmetric exclusion process (TASEP) [J. Stat. Mech. (2012) P05014] is an integrable generalization of the TASEP equipped with an interaction, which enhances the clustering of particles. The process interpolates between two extremal cases: the TASEP with parallel update and the process with all particles irreversibly merging into a single cluster moving as an isolated particle. We are interested in the large time behavior of this process on a ring in the whole range of the parameter λ controlling the interaction. We study the stationary state correlations, the cluster size distribution, and the large-time fluctuations of integrated particle current. When λ is finite, we find the usual TASEP-like behavior: The correlation length is finite; there are only clusters of finite size in the stationary state and current fluctuations belong to the Kardar-Parisi-Zhang universality class. When λ grows with the system size, so does the correlation length. We find a nontrivial transition regime with clusters of all sizes on the lattice. We identify a crossover parameter and derive the large deviation function for particle current, which interpolates between the case considered by Derrida-Lebowitz and a single-particle diffusion.

Exclusive queueing processes and their application to traffic systems

Pedestrian queues like those observed at ticket counters or supermarket checkouts are usually described by classical queueing theory. However, models like the M/M/1 queue neglect the internal structure (density profile) of the queue by focussing on the system length as the only dynamical variable. This is different in the Exclusive Queueing Process (EQP) in which the queue is considered on a microscopic level. It is equivalent to a Totally Asymmetric Exclusion Process (TASEP) of varying length. The EQP has a surprisingly rich phase diagram with respect to the arrival probability α and the service probability β. The behavior on the phase transition line is much more complex than for the TASEP with a fixed system length. It is nonuniversal and depends strongly on the update procedure used. In this paper, we review the main properties of the EQP and its applications to pedestrian dynamics, vehicular traffic and biological systems. We also mention extensions of the EQP and some related models.

Boundary induced phase transition with stochastic entrance and exit

.We study an open-chain totally asymmetric exclusion process (TASEP) with stochastic gates present at the two boundaries. The gating dynamics has been modeled with the physical system of ion-channel gating in mind. These gates can randomly switch between an open state and a closed state. In the open state, the gates are highly permeable such that any particle arriving at the gate immediately passes through. In the closed state, a particle becomes trapped at the gate and cannot pass through until the gate switches open again. We calculate the phase-diagram of the system and find important and non-trivial differences with the phase-diagram of a regular open-chain TASEP. In particular, depending on the switching rates of the two gates, the system may or may not admit a maximal current phase. Our analytic calculations within mean-field theory capture the main qualitative features of our Monte Carlo simulation results. We also perform a refined mean-field calculation where the correlations at the boundaries are taken into account. This theory shows significantly better quantitative agreement with our simulation results.

Exact domain wall theory for deterministic TASEP with parallel update

We develop an exact domain wall theory (DWT) for the totally asymmetric exclusion process (TASEP) with parallel update and deterministic (p = 1) bulk motion. Remarkably, the dynamics of this system can be described by the motion of a domain wall not only on the coarse-grained level but also exactly on the microscopic scale for arbitrary system size. All properties of this TASEP, not only stationary but also time-dependent, are shown to follow from the solution of a bivariate master equation whose variables are not only the position but also the velocity of the domain wall. In the continuum limit this exactly soluble model then allows us to perform a first principle derivation of a Fokker–Planck equation for the position of the wall.

The Dynamics of Waiting: The Exclusive Queueing Process

The dynamics of pedestrian crowds has been studied intensively in recent years, both theoretically and empirically. However, in many situations pedestrian movement is rather static, e.g. due to jamming near bottlenecks or queueing at ticket counters or the su- permarket checkout. Classically such queues are described by a M/M/1 queue which neglects the internal structure (density profile) of the queue by focussing on the queue length as the only dynamical variable. This is different in the exclusive queueing process (EQP) which considers the queue on a microscopic level. It is equivalent to a totally asymmetric exclusion process (TASEP) of varying length for which many exact results can be obtained. The EQP has a surprisingly rich phase diagram with respect to the arrival probability α and the service probability β The behaviour at the phase transition line is much more complex than for the TASEP. It is nonuniversal and depends strongly on the update procedure used.

Accelerated transport and growth with symmetrized dynamics

In this paper we consider a model of accelerated dynamics with the rules modified from those of the recently proposed [Dong et al., Phys. Rev. Lett. 109, 130602 (2012)] accelerated exclusion process (AEP) such that particle-vacancy symmetry is restored to facilitate a mapping to a solid-on-solid growth model in 1+1 dimensions. In addition to kicking a particle ahead of the moving particle, as in the AEP, in our model another particle from behind is drawn, provided it is within the "distance of interaction" denoted by ℓ(max). We call our model the doubly accelerated exclusion process (DAEP). We observe accelerated transport and interface growth and widening of the cluster size distribution for cluster sizes above ℓ(max), when compared with the ordinary totally asymmetric exclusion process (TASEP). We also characterize the difference between the TASEP, AEP, and DAEP by computing a "staggered" order parameter, which reveals the local order in the steady state. This order in part explains the behavior of the particle current as a function of density. The differences of the steady states are also reflected by the behavior of the temporal and spatial correlation functions in the interface picture.

Critical behavior of the exclusive queueing process

The exclusive queueing process (EQP) is a generalization of the classical M/M/1 queue. It is equivalent to a totally asymmetric exclusion process (TASEP) of varying length. Here we consider two discrete-time versions of the EQP with parallel and backward-sequential update rules. The phase diagram (with respect to the arrival probability α and the service probability β) is divided into two phases corresponding to divergence and convergence of the system length. We investigate the behavior on the critical line separating these phases. For both update rules, we find diffusive behavior for small service probability . However, for it becomes sub-diffusive and nonuniversal: the critical exponents characterizing the divergence of the system length and the number of customers are found to depend on the update rule. For the backward-update case, they also depend on the hopping parameter p, and remain finite when p is large, indicating a first-order transition.