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Register a new userTASEP on parallel tracks: effects of mobile bottlenecks in fixed segments
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Added by
Debashish Chowdhury
Publication date
2014
fields
Physics
and research's language is
English
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We study the flux of totally asymmetric simple exclusion processes (TASEPs) on a twin co-axial square tracks. In this biologically motivated model the particles in each track act as mobile bottlenecks against the movement of the particles in the other although the particle are not allowed to move out of their respective tracks. So far as the outer track is concerned, the particles on the inner track act as bottlenecks only over a set of fixed segments of the outer track, in contrast to site-associated and particle-associated quenched randomness in the earlier models of disordered TASEP. In a special limiting situation the movement of particles in the outer track mimic a TASEP with a point-like immobile (i.e., quenched) defect where phase segregation of the particles is known to take place. The length of the inner track as well as the strength and number density of the mobile bottlenecks moving on it are the control parameters that determine the nature of spatio-temporal organization of particles on the outer track. Variation of these control parameters allow variation of the width of the phase-coexistence region on the flux-density plane of the outer track. Some of these phenomena are likely to survive even in the future extensions intended for studying traffic-like collective phenomena of polymerase motors on double-stranded DNA.
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Domain wall theory (DWT) has proved to be a powerful tool for the analysis of one-dimensional transport processes. A simple version of it was found very accurate for the Totally Asymmetric Simple Exclusion Process (TASEP) with random sequential update. However, a general implementation of DWT is still missing in the case of updates with less fluctuations, which are often more relevant for applications. Here we develop an exact DWT for 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, time-dependent and stationary, 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 diffusion constant appearing in this equation differs from the one obtained with the traditional `simple DWT.
Totally asymmetric simple exclusion process (TASEP) was originally introduced as a model for the traffic-like collective movement of ribosomes on a messenger RNA (mRNA) that serves as the track for the motor-like forward stepping of individual ribosomes. In each step, a ribosome elongates a protein by a single unit using the track also as a template for protein synthesis. But, pre-fabricated, functionally competent, ribosomes are not available to begin synthesis of protein; a subunit directionally scans the mRNA in search of the pre-designated site where it is supposed to bind with the other subunit and begin the synthesis of the corresponding protein. However, because of `leaky scanning, a fraction of the scanning subunits miss the target site and continue their search beyond the first target. Sometimes such scanners successfully identify the site that marks the site for initiation of the synthesis of a different protein. In this paper, we develop an exclusion model, with three interconvertible species of hard rods, to capture some of the key features of these biological phenomena and study the effects of the interference of the flow of the different species of rods on the same lattice. More specifically, we identify the meantime for the initiation of protein synthesis as appropriate mean {it first-passage} time that we calculate analytically using the formalism of backward master equations. In spite of the approximations made, our analytical predictions are in reasonably good agreement with the numerical data that we obtain by performing Monte Carlo simulations. We also compare our results with a few experimental facts reported in the literature and propose new experiments for testing some of our new quantitative predictions.
We study the collective escape dynamics of a chain of coupled, weakly damped nonlinear oscillators from a metastable state over a barrier when driven by a thermal heat bath in combination with a weak, globally acting periodic perturbation. Optimal parameter choices are identified that lead to a drastic enhancement of escape rates as compared to a pure noise-assisted situation. We elucidate the speed-up of escape in the driven Langevin dynamics by showing that the time-periodic external field in combination with the thermal fluctuations triggers an instability mechanism of the stationary homogeneous lattice state of the system. Perturbations of the latter provided by incoherent thermal fluctuations grow because of a parametric resonance, leading to the formation of spatially localized modes (LMs). Remarkably, the LMs persist in spite of continuously impacting thermal noise. The average escape time assumes a distinct minimum by either tuning the coupling strength and/or the driving frequency. This weak ac-driven assisted escape in turn implies a giant speed of the activation rate of such thermally driven coupled nonlinear oscillator chains.
The well known Sandpile model of self-organized criticality generates avalanches of all length and time scales, without tuning any parameters. In the original models the external drive is randomly selected. Here we investigate a drive which depends on the present state of the system, namely the effect of favoring sites with a certain height in the deposition process. If sites with height three are favored, the system stays in a critical state. Our numerical results indicate the same universality class as the original model with random depositition, although the stationary state is approached very differently. In constrast, when favoring sites with height two, only avalanches which cover the entire system occur. Furthermore, we investigate the distributions of sites with a certain height, as well as the transient processes of the different variants of the external drive.
Motivated by interest in pedestrian traffic we study two lanes (one-dimensional lattices) of length $L$ that intersect at a single site. Each lane is modeled by a TASEP (Totally Asymmetric Exclusion Process). The particles enter and leave lane $sigma$ (where $sigma=1,2$) with probabilities $alpha_sigma$ and $beta_sigma$, respectively. We employ the `frozen shuffle update introduced in earlier work [C. Appert-Rolland et al, J. Stat. Mech. (2011) P07009], in which the particle positions are updated in a fixed random order. We find analytically that each lane may be in a `free flow or in a `jammed state. Hence the phase diagram in the domain $0leqalpha_1,alpha_2leq 1$ consists of four regions with boundaries depending on $beta_1$ and $beta_2$. The regions meet in a single point on the diagonal of the domain. Our analytical predictions for the phase boundaries as well as for the currents and densities in each phase are confirmed by Monte Carlo simulations.
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