Unlike equilibrium statistical mechanics, with its well-established foundations, a similar widely accepted framework for non-equilibrium statistical mechanics (NESM) remains elusive. Here, we review some of the many recent activities on NESM, focusing on some of the fundamental issues and general aspects. Using the language of stochastic Markov processes, we emphasize general properties of the evolution of configurational probabilities, as described by master equations. Of particular interest are systems in which the dynamics violates detailed balance, since such systems serve to model a wide variety of phenomena in nature. We next review two distinct approaches for investigating such problems. One approach focuses on models sufficiently simple to allow us to find exact, analytic, non-trivial results. We provide detailed mathematical analyses of a one-dimensional continuous-time lattice gas, the totally asymmetric exclusion process. It is regarded as a paradigmatic model for NESM, much like the role the Ising model played for equilibrium statistical mechanics. It is also the starting point for the second approach, which attempts to include more realistic ingredients in order to be more applicable to systems in nature. Restricting ourselves to the area of biophysics and cellular biology, we review a number of models that are relevant for transport phenomena. Successes and limitations of these simple models are also highlighted.

/pdf/non-equilibrium-statistical-mechanics-from-a-paradigmatic-1gq17no141.pdf

Non-equilibrium statistical mechanics: from a paradigmatic model to biological transport

Unlike equilibrium statistical mechanics, with its well-established foundations, a similar widely-accepted framework for non-equilibrium statistical mechanics (NESM) remains elusive. Here, we review some of the many recent activities on NESM, focusing on some of the fundamental issues and general aspects. Using the language of stochastic Markov processes, we emphasize general properties of the evolution of configurational probabilities, as described by master equations. Of particular interest are systems in which the dynamics violate detailed balance, since such systems serve to model a wide variety of phenomena in nature. We next review two distinct approaches for investigating such problems. One approach focuses on models sufficiently simple to allow us to find exact, analytic, non-trivial results. We provide detailed mathematical analyses of a one-dimensional continuous-time lattice gas, the totally asymmetric exclusion process (TASEP). It is regarded as a paradigmatic model for NESM, much like the role the Ising model played for equilibrium statistical mechanics. It is also the starting point for the second approach, which attempts to include more realistic ingredients in order to be more applicable to systems in nature. Restricting ourselves to the area of biophysics and cellular biology, we review a number of models that are relevant for transport phenomena. Successes and limitations of these simple models are also highlighted.

Non-equilibrium statistical mechanics: From a paradigmatic model to biological transport

The process of protein synthesis in biological systems resembles a one dimensional driven lattice gas in which the particles have spatial extent, covering more than one lattice site. We expand the well studied totally asymmetric exclusion process, in which particles typically cover a single lattice site, to include cases with extended objects. Exact solutions can be determined for a uniform closed system. We analyze the uniform open system through two approaches. First, a continuum limit produces a modified diffusion equation for particle density profiles. Second, an extremal principle based on domain wall theory accurately predicts the phase diagram and currents in each phase. Finally, we briefly consider approximate approaches to a nonuniform open system with quenched disorder in the particle hopping rates and compare these approaches with Monte Carlo simulations.

/pdf/totally-asymmetric-exclusion-process-with-extended-objects-a-3p5ualihen.pdf

Totally asymmetric exclusion process with extended objects: a model for protein synthesis.

The steady-state currents and densities of a one-dimensional totally asymmetric exclusion process (TASEP) with particles that occlude an integer number (d) of lattice sites are computed using various mean-field approximations and Monte Carlo simulations. TASEPs featuring particles of arbitrary size are relevant for modelling systems such as mRNA translation, vesicle locomotion along microtubules and protein sliding along DNA. We conjecture that the nonequilibrium steady-state properties separate into low-density, high-density, and maximal current phases similar to those of the standard (d = 1) TASEP. A simple mean-field approximation for steady-state particle currents and densities is found to be inaccurate. However, we find local equilibrium particle distributions derived from a discrete Tonks gas partition function yield apparently exact currents within the maximal current phase. For the boundary-limited phases, the equilibrium Tonks gas distribution cannot be used to predict currents, phase boundaries, or the order of the phase transitions. However, we employ a refined mean-field approach to find apparently exact expressions for the steady-state currents, boundary densities, and phase diagrams of the d ≥ 1 TASEP. Extensive Monte Carlo simulations are performed to support our analytic, mean-field results.

Totally asymmetric exclusion processes with particles of arbitrary size

Recent work on stochastic interacting particle systems with two particle species (or single-species systems with kinematic constraints) has demonstrated the existence of spontaneous symmetry breaking, long-range order and phase coexistence in nonequilibrium steady states, even if translational invariance is not broken by defects or open boundaries. If both particle species are conserved, the temporal behaviour is largely unexplored, but first results of current work on the transition from the microscopic to the macroscopic scale yield exact coupled nonlinear hydrodynamic equations and indicate the emergence of novel types of shock waves which are collective excitations stabilized by the flow of microscopic fluctuations. We review the basic stationary and dynamic properties of these systems, highlighting the role of conservation laws and kinetic constraints for the hydrodynamic behaviour, the microscopic origin of domain wall (shock) stability and the coarsening dynamics of domains during phase separation.

Critical phenomena and universal dynamics in one-dimensional driven diffusive systems with two species of particles

A generalization of the simple exclusion asymmetric model is introduced. In this model an arbitrary mixture of molecules with distinct sizes $s=0,1,2,\dots{},$ in units of lattice space, diffuses asymmetrically on the lattice. A related surface growth model is also presented. Variations of the distribution of the molecules sizes may change the excluded volume almost continuously. We solve the model exactly through the Bethe ansatz and the dynamical critical exponent z is calculated from the finite-size corrections of the mass gap of the related quantum chain. Our results show that for an arbitrary distribution of molecules, the dynamical critical behavior is on the Kardar-Parizi-Zhang universality.

https://arxiv.org/pdf/cond-mat/9904130.pdf

Exact solution of the asymmetric exclusion model with particles of arbitrary size.

The exact solution of the asymmetric exclusion problem with first- and scond-class particles is presented. In this model the particles (size 1) of both classes are located at lattice points, and diffuse with equal asymmetric rates, but particles in the first class do not distinguish those in the second class from holes (empty sites). We generalize and solve exactly this model by considering molecules in the first and second class with sizes s1 and s2 (s1, s2 = 0, 1, 2, ...), in units of lattice spacing, respectively. The solution is derived by a Bethe ansatz of nested type. We give a simple pedagogical presentation of the Bethe ansatz solution of the problem which can easily be followed by a reader not specialized in exactly integrable models.

/pdf/exact-solution-of-asymmetric-diffusion-with-second-class-eel6c5xmcd.pdf

Exact solution of asymmetric diffusion with second-class particles of arbitrary size

New exactly integrable quantum spin-1 chains are derived. These new quantum Hamiltonians, like the XXZ chain, have a free parameter (anisotropy) and commute with the z-component of the total magnetization. The eigenvalues and eigenvectors are obtained directly by imposing a generalized coordinate Bethe ansatz. The derived Bethe ansatz equations have an unusual form and the associated R-matrix, has a dependence with the spectral parameter that is not of difference form, like the Hubbard quantum chain.

R.Z. Bariev

Papers

Exact solution of the asymmetric exclusion model with particles of arbitrary size.

Exact solution of asymmetric diffusion with second-class particles of arbitrary size

New exact integrable spin-1 quantum chains

On the rotational symmetry of the spin-spin correlation function of the two-dimensional Ising model

Many-point correlation functions of the two-dimensional Ising model