The asymmetric exclusion model with sequential update

We present a solution for the stationary state of an asymmetric exclusion model with sequential update and open boundary conditions. We solve the model exactly for random hopping in both directions by applying a matrix-product formalism which was recently used to solve the model with sublattice-parallel update[1]. It is shown that the matrix-algebra describing the sequential update and sublattice-parallel update are identical and can be mapped onto the random sequential case treated by Derrida et al[2].Comment: 7 pages, Late

Exact density profiles for fully asymmetric exclusion process with discrete-time dynamics

Exact density profiles in the steady state of the one-dimensional fully asymmetric simple exclusion process on semi-infinite chains are obtained in the case of forward-ordered sequential dynamics by taking the thermodynamic limit in our recent exact results for a finite chain with open boundaries. The corresponding results for sublattice parallel dynamics follow from the relationship obtained by Rajewsky and Schreckenberg [Physica A 245, 139 (1997)] and for parallel dynamics from the mapping found by Evans, Rajewsky and Speer [J. Stat. Phys. 95, 45 (1999)]. By comparing the asymptotic results appropriate for parallel update with those published in the latter paper, we correct some technical errors in the final results given there.Comment: About 10 pages and 3 figures, new references are added and a comparison is made with the results by de Gier and Nienhuis [Phys. Rev. E 59, 4899(1999)

Phase Transition in a Three-States Reaction-Diffusion System

A one-dimensional reaction-diffusion model consisting of two species of particles and vacancies on a ring is introduced. The number of particles in one species is conserved while in the other species it can fluctuate because of creation and annihilation of particles. It has been shown that the model undergoes a continuous phase transition from a phase where the currents of different species of particles are equal to another phase in which they are different. The total density of particles and also their currents in each phase are calculated exactly.Comment: 6 page

Mixed messages: re-initiation factors regulate translation of animal mRNAs

When ribosomes encounter upstream open reading frames (uORFs) during scanning of the 5' untranslated region (5' UTR), translation of the downstream ORF requires re-initiation. In a recent paper in Nature, Schleich et al. describe metazoan factors which specifically promote re-initiation

Exact solution of an exclusion process with three classes of particles and vacancies

We present an exact solution for an asymmetric exclusion process on a ring with three classes of particles and vacancies. Using a matrix product Ansatz, we find explicit expressions for the weights of the configurations in the stationary state. The solution involves tensor products of quadratic algebras.Comment: 18 pages, no figures, LaTe

Application of the Density Matrix Renormalization Group Method to a Non-Equilibrium Problem

We apply the density matrix renormalization group (DMRG) method to a non-equilibrium problem: the asymmetric exclusion process in one dimension. We study the stationary state of the process to calculate the particle density profile (one-point function). We show that, even with a small number of retained bases, the DMRG calculation is in excellent agreement with the exact solution obtained by the matrix-product-ansatz approach.Comment: 8 pages, LaTeX (using jpsj.sty), 4 non-embedded figures, submitted to J. Phys. Soc. Jp

Exact solution of the Bernoulli matching model of sequence alignment

Through a series of exact mappings we reinterpret the Bernoulli model of sequence alignment in terms of the discrete-time totally asymmetric exclusion process with backward sequential update and step function initial condition. Using earlier results from the Bethe ansatz we obtain analytically the exact distribution of the length of the longest common subsequence of two sequences of finite lengths $X,Y$. Asymptotic analysis adapted from random matrix theory allows us to derive the thermodynamic limit directly from the finite-size result.Comment: 13 pages, 4 figure

Stochastic boundary conditions in the deterministic Nagel-Schreckenberg traffic model

We consider open systems where cars move according to the deterministic Nagel-Schreckenberg rules and with maximum velocity ${v}_{max} > 1$, what is an extension of the Asymmetric Exclusion Process (ASEP). It turns out that the behaviour of the system is dominated by two features: a) the competition between the left and the right boundary b) the development of so-called "buffers" due to the hindrance an injected car feels from the front car at the beginning of the system. As a consequence, there is a first-order phase transition between the free flow and the congested phase accompanied by the collapse of the buffers and the phase diagram essentially differs from that of ${v}_{max} = 1$ (ASEP).Comment: 29 pages, 26 figure

An Exactly Solvable Two-Way Traffic Model With Ordered Sequential Update

Within the formalism of matrix product ansatz, we study a two-species asymmetric exclusion process with backward and forward site-ordered sequential update. This model, which was originally introduced with the random sequential update, describes a two-way traffic flow with a dynamic impurity and shows a phase transition between the free flow and traffic jam. We investigate the characteristics of this jamming and examine similarities and differences between our results and those with random sequential update.Comment: 25 pages, Revtex, 7 ps file

Direct in vivo V(H) to J(H) rearrangement violating the 12/23 rule

V(D)J recombination at the immunoglobulin heavy chain (IgH) locus follows the 12/23 rule to ensure the correct assembly of the variable region gene segments. Here, we report characterization of an in vivo model that allowed us to study recombination violating the 12/23 rule, namely a mouse strain lacking canonical D elements in its IgH locus. We demonstrate that V(H) to J(H) joining can support the generation of all B cell subsets. However, the process is inefficient in that B cells and antibodies derived from the D(H)-less allele are not detectable if the latter is combined with a wild-type IgH allele. There is no preferential usage of any particular V(H) gene family or J(H) element in V(H)J(H) junctions, indicating that 23/23-guided recombination is possible, but is a low frequency event at the IgH locus in vivo