Driven k-mers: correlations in space and time

An exactly solvable model for RNA polymerase during the elongation stage

We consider a Markovian model for the kinetics of RNA Polymerase (RNAP) which provides a physical explanation for the phenomenon of cooperative pushing during transcription elongation observed in biochemical experiments onEscherichia coliand yeast RNAP. To study how backtracking of RNAP affects cooperative pushing we incorporate into this model backward (upstream) RNAP moves. With a rigorous mathematical treatment of the model we derive conditions on the mutual static and kinetic interactions between RNAP under which backtracking preserves cooperative pushing. This is achieved by exact computation of several key properties in the steady state of this model, including the distribution of headway between two RNAP along the DNA template and the average RNAP velocity and flux.

Short-range and long-range correlations in driven dense colloidal mixtures in narrow pores

The system of a driven dense colloid mixture in a tube with diameter comparable to particle size is modeled by a generalization of the asymmetric simple exclusion process (ASEP) model. The generalization goes in two directions: relaxing the exclusion constraint by allowing several (but few) particles on a site and by considering two species of particles, which differ in size and transport coefficients. We calculate the nearest-neighbor correlations using a variant of the Kirkwood approximation and show by comparison with numerical simulations that the approximation provides quite accurate results. However, for long-range correlations, we show that the Kirkwood approximation is useless, as it predicts exponential decay of the density-density correlation function with distance, while simulation data indicate that the decay is algebraic. For the one-component system, we show that the decay is governed by a power law with universal exponent close to 2. In the two-component system, the correlation function behaves in a more complicated manner: Its sign oscillates but the envelope decays again very slowly and the decay is compatible with a power law with an exponent somewhat lower than 2. Therefore, our generalization of the ASEP belongs to a different universality class from the ensemble of generalized ASEP models which are mappable to zero-range processes.

Roughening of k-mer-growing interfaces in stationary regimes

We discuss the steady-state dynamics of interfaces with periodic boundary conditions arising from body-centered solid-on-solid growth models in 1+1 dimensions involving random aggregation of extended particles (dimers, trimers, ...,k-mers). Roughening exponents as well as width and maximal height distributions can be evaluated directly in stationary regimes by mapping the dynamics onto an asymmetric simple exclusion process with k-type of vacancies. Although for k≥2 the dynamics is partitioned into an exponentially large number of sectors of motion, the results obtained in some generic cases strongly suggest a universal scaling behavior closely following that of monomer interfaces.

Phase coexistence and spatial correlations in reconstituting k-mer models

In reconstituting k-mer models, extended objects that occupy several sites on a one-dimensional lattice undergo directed or undirected diffusion, and reconstitute-when in contact-by transferring a single monomer unit from one k-mer to the other; the rates depend on the size of participating k-mers. This polydispersed system has two conserved quantities, the number of k-mers and the packing fraction. We provide a matrix product method to write the steady state of this model and to calculate the spatial correlation functions analytically. We show that for a constant reconstitution rate, the spatial correlation exhibits damped oscillations in some density regions separated, from other regions with exponential decay, by a disorder surface. In a specific limit, this constant-rate reconstitution model is equivalent to a single dimer model and exhibits a phase coexistence similar to the one observed earlier in totally asymmetric simple exclusion process on a ring with a defect.

Exponential decay of spatial correlation in driven diffusive system: A universal feature of macroscopic homogeneous state

Driven diffusive systems have been a paradigm for modelling many physical, chemical, and biological transport processes. In the systems, spatial correlation plays an important role in the emergence of a variety of nonequilibrium phenomena and exhibits rich features such as pronounced oscillations. However, the lack of analytical results of spatial correlation precludes us from fully understanding the effect of spatial correlation on the dynamics of the system. Here we offer precise analytical predictions of the spatial correlation in a typical driven diffusive system, namely facilitated asymmetric exclusion process. We find theoretically that the correlation between two sites decays exponentially as their distance increases, which is in good agreement with numerical simulations. Furthermore, we find the exponential decay is a universal property of macroscopic homogeneous state in a broad class of 1D driven diffusive systems. Our findings deepen the understanding of many nonequilibrium phenomena resulting from spatial correlation in driven diffusive systems.

Cluster-factorized steady states in finite-range processes

We study a class of nonequilibrium lattice models on a ring where particles hop in a particular direction, from a site to one of its (say, right) nearest neighbors, with a rate that depends on the occupation of all the neighboring sites within a range R. This finite-range process (FRP) for R=0 reduces to the well-known zero-range process (ZRP), giving rise to a factorized steady state (FSS) for any arbitrary hop rate. We show that, provided the hop rates satisfy a specific condition, the steady state of FRP can be written as a product of a cluster-weight function of (R+1) occupation variables. We show that, for a large class of cluster-weight functions, the cluster-factorized steady state admits a finite dimensional transfer-matrix formulation, which helps in calculating the spatial correlation functions and subsystem mass distributions exactly. We also discuss a criterion for which the FRP undergoes a condensation transition.

Simulations of driven and reconstituting lattice gases

We discuss stationary aspects of a set of driven lattice gases in which hard-core particles with spatial extent, covering more than one lattice site, diffuse and reconstruct in one dimension under nearest-neighbor interactions. As in the uncoupled case [M. Barma et al., J. Phys.: Condens. Matter 19, 065112 (2007)], the dynamics of the phase space breaks up into an exponentially large number of mutually disconnected sectors labeled by a nonlocal construct, the irreducible string. Depending on whether the particle couplings are taken attractive or repulsive, simulations in most of the studied sectors show that both steady state currents and pair correlations behave quite differently at low temperature regimes. For repulsive interactions an order-by-disorder transition is suggested.