Towards a model for protein production rates

In the process of translation, ribosomes read the genetic code on an mRNA and assemble the corresponding polypeptide chain. The ribosomes perform discrete directed motion which is well modeled by a totally asymmetric simple exclusion process (TASEP) with open boundaries. Using Monte Carlo simulations and a simple mean-field theory, we discuss the effect of one or two ``bottlenecks'' (i.e., slow codons) on the production rate of the final protein. Confirming and extending previous work by Chou and Lakatos, we find that the location and spacing of the slow codons can affect the production rate quite dramatically. In particular, we observe a novel ``edge'' effect, i.e., an interaction of a single slow codon with the system boundary. We focus in detail on ribosome density profiles and provide a simple explanation for the length scale which controls the range of these interactions.Comment: 8 pages, 8 figure

Localized defects in a cellular automaton model for traffic flow with phase separation

We study the impact of a localized defect in a cellular automaton model for traffic flow which exhibits metastable states and phase separation. The defect is implemented by locally limiting the maximal possible flow through an increase of the deceleration probability. Depending on the magnitude of the defect three phases can be identified in the system. One of these phases shows the characteristics of stop-and-go traffic which can not be found in the model without lattice defect. Thus our results provide evidence that even in a model with strong phase separation stop-and-go traffic can occur if local defects exist. From a physical point of view the model describes the competition between two mechanisms of phase separation.Comment: 14 pages, 7 figure

Reconstruction on trees and spin glass transition

Consider an information source generating a symbol at the root of a tree network whose links correspond to noisy communication channels, and broadcasting it through the network. We study the problem of reconstructing the transmitted symbol from the information received at the leaves. In the large system limit, reconstruction is possible when the channel noise is smaller than a threshold. We show that this threshold coincides with the dynamical (replica symmetry breaking) glass transition for an associated statistical physics problem. Motivated by this correspondence, we derive a variational principle which implies new rigorous bounds on the reconstruction threshold. Finally, we apply a standard numerical procedure used in statistical physics, to predict the reconstruction thresholds in various channels. In particular, we prove a bound on the reconstruction problem for the antiferromagnetic ``Potts'' channels, which implies, in the noiseless limit, new results on random proper colorings of infinite regular trees. This relation to the reconstruction problem also offers interesting perspective for putting on a clean mathematical basis the theory of glasses on random graphs.Comment: 34 pages, 16 eps figure

A multi-species asymmetric simple exclusion process and its relation to traffic flow

Using the matrix product formalism we formulate a natural p-species generalization of the asymmetric simple exclusion process. In this model particles hop with their own specific rate and fast particles can overtake slow ones with a rate equal to their relative speed. We obtain the algebraic structure and study the properties of the representations in detail. The uncorrelated steady state for the open system is obtained and in the ($p \to \infty)$ limit, the dependence of its characteristics on the distribution of velocities is determined. It is shown that when the total arrival rate of particles exceeds a certain value, the density of the slowest particles rises abroptly.Comment: some typos corrected, references adde

Exact solutions for a mean-field Abelian sandpile

We introduce a model for a sandpile, with N sites, critical height N and each site connected to every other site. It is thus a mean-field model in the spin-glass sense. We find an exact solution for the steady state probability distribution of avalanche sizes, and discuss its asymptotics for large N.Comment: 10 pages, LaTe

Effect of a columnar defect on the shape of slow-combustion fronts

We report experimental results for the behavior of slow-combustion fronts in the presence of a columnar defect with excess or reduced driving, and compare them with those of mean-field theory. We also compare them with simulation results for an analogous problem of driven flow of particles with hard-core repulsion (ASEP) and a single defect bond with a different hopping probability. The difference in the shape of the front profiles for excess vs. reduced driving in the defect, clearly demonstrates the existence of a KPZ-type of nonlinear term in the effective evolution equation for the slow-combustion fronts. We also find that slow-combustion fronts display a faceted form for large enough excess driving, and that there is a corresponding increase then in the average front speed. This increase in the average front speed disappears at a non-zero excess driving in agreement with the simulated behavior of the ASEP model.Comment: 7 pages, 7 figure

Driven Lattice Gases with Quenched Disorder: Exact Results and Different Macroscopic Regimes

We study the effect of quenched spatial disorder on the steady states of driven systems of interacting particles. Two sorts of models are studied: disordered drop-push processes and their generalizations, and the disordered asymmetric simple exclusion process. We write down the exact steady-state measure, and consequently a number of physical quantities explicitly, for the drop-push dynamics in any dimensions for arbitrary disorder. We find that three qualitatively different regimes of behaviour are possible in 1-$d$ disordered driven systems. In the Vanishing-Current regime, the steady-state current approaches zero in the thermodynamic limit. A system with a non-zero current can either be in the Homogeneous regime, chracterized by a single macroscopic density, or the Segregated-Density regime, with macroscopic regions of different densities. We comment on certain important constraints to be taken care of in any field theory of disordered systems.Comment: RevTex, 17pages, 18 figures included using psfig.st

Phase Separation in One-Dimensional Driven Diffusive Systems

A driven diffusive model of three types of particles that exhibits phase separation on a ring is introduced. The dynamics is local and comprises nearest neighbor exchanges that conserve each of the three species. For the case in which the three densities are equal, it is shown that the model obeys detailed balance. The Hamiltonian governing the steady state distribution in this case is given and is found to have long range asymmetric interactions. The partition sum and bounds on some correlation functions are calculated analytically demonstrating phase separation.Comment: 4 Pages, Revtex, 2 Figures included, Submitted to Physical Review Letter

Abelian Sandpile Model on the Husimi Lattice of Square Plaquettes

An Abelian sandpile model is considered on the Husimi lattice of square plaquettes. Exact expressions for the distribution of height probabilities in the Self-Organized Critical state are derived. The two-point correlation function for the sites deep inside the Husimi lattice is calculated exactly.Comment: 12 pages, LaTeX, source files and some additional information available at http://thsun1.jinr.dubna.su/~shcher

Anisotropic Diffusion-Limited Reactions with Coagulation and Annihilation

One-dimensional reaction-diffusion models A+A -> 0, A+A -> A, and $A+B -> 0, where in the latter case like particles coagulate on encounters and move as clusters, are solved exactly with anisotropic hopping rates and assuming synchronous dynamics. Asymptotic large-time results for particle densities are derived and discussed in the framework of universality.Comment: 13 pages in plain Te