Steady-state properties of a totally asymmetric exclusion process with periodic structure

Polysomally protected viruses

It is conceivable that an RNA virus could use a polysome, that is, a string of ribosomes covering the RNA strand, to protect the genetic material from degradation inside a host cell. This paper discusses how such a virus might operate, and how its presence might be detected by ribosome profiling. There are two possible forms for such apolysomally protected virus, depending upon whether just the forward strand or both the forward and complementary strands can be encased by ribosomes (these will be termed type 1 and type 2, respectively). It is argued that in the type 2 case the viral RNA would evolve anambigrammaticproperty, whereby the viral genes are free of stop codons in a reverse reading frame (with forward and reverse codons aligned). Recent observations of ribosome profiles of ambigrammatic narnavirus sequences are consistent with our predictions for the type 2 case.

Asymmetric simple exclusion process with position-dependent hopping rates: Phase diagram from boundary-layer analysis

In this paper, we study a one-dimensional totally asymmetric simple exclusion process with position-dependent hopping rates. Under open boundary conditions, this system exhibits boundary-induced phase transitions in the steady state. Similarly to totally asymmetric simple exclusion processes with uniform hopping, the phase diagram consists of low-density, high-density, and maximal-current phases. In various phases, the shape of the average particle density profile across the lattice including its boundary-layer parts changes significantly. Using the tools of boundary-layer analysis, we obtain explicit solutions for the density profile in different phases. A detailed analysis of these solutions under different boundary conditions helps us obtain the equations for various phase boundaries. Next, we show how the shape of the entire density profile including the location of the boundary layers can be predicted from the fixed points of the differential equation describing the boundary layers. We discuss this in detail through several examples of density profiles in various phases. The maximal-current phase appears to be an especially interesting phase where the boundary layer flows to a bifurcation point on the fixed-point diagram.

Interference of two codirectional exclusion processes in the presence of a static bottleneck: A biologically motivated model

We develop a two-species exclusion process with a distinct pair of entry and exit sites for each species of rigid rods. The relatively slower forward stepping of the rods in an extended bottleneck region, located in between the two entry sites, controls the extent of interference of the codirectional flow of the two species of rods. The relative positions of the sites of entry of the two species of rods with respect to the location of the bottleneck are motivated by a biological phenomenon. However, the primary focus of the study here is to explore the effects of the interference of the flow of the two species of rods on their spatiotemporal organization and the regulations of this interference by the extended bottleneck. By a combination of mean-field theory and computer simulation, we calculate the flux of both species of rods and their density profiles as well as the composite phase diagrams of the system. If the bottleneck is sufficiently stringent, then some of the phases become practically unrealizable, although not ruled out on the basis of any fundamental physical principle. Moreover, the extent of suppression of flow of the downstream entrants by the flow of the upstream entrants can also be regulated by the strength of the bottleneck. We speculate on the possible implications of the results in the context of the biological phenomenon that motivated the formulation of the theoretical model.

Nonequilibrium Diffusion and Capture Mechanism Ensures Tip Localization of Regulating Proteins on Dynamic Filaments

Diffusive motion of regulatory enzymes on biopolymers with eventual capture at a reaction site is a common feature in cell biology. Using a lattice gas model we study the impact of diffusion and capture for a microtubule polymerase and a depolymerase. Our results show that the capture mechanism localizes the proteins and creates large-scale spatial correlations. We develop an analytic approximation that globally accounts for relevant correlations and yields results that are in excellent agreement with experimental data. Our results show that diffusion and capture operates most efficiently at cellular enzyme concentrations which points to in vivo relevance.

Sensitivity of mRNA Translation

Using the dynamic mean-field approximation of the totally asymmetric simple exclusion process (TASEP), we investigate the effect of small changes in the initiation, elongation, and termination rates along the mRNA strand on the steady-state protein translation rate. We show that the sensitivity of mRNA translation is equal to the sensitivity of the maximal eigenvalue of a symmetric, nonnegative, tridiagonal, and irreducible matrix. This leads to new analytical results as well as efficient numerical schemes that are applicable for large-scale models. Our results show that in the usual endogenous case, when initiation is more rate-limiting than elongation, the sensitivity of the translation rate to small mutations rapidly increases towards the 5′ end of the ORF. When the initiation rate is high, as may be the case for highly expressed and/or heterologous optimized genes, the maximal sensitivity is with respect to the elongation rates at the middle of the mRNA strand. We also show that the maximal possible effect of a small increase/decrease in any of the rates along the mRNA is an increase/decrease of the same magnitude in the translation rate. These results are in agreement with previous molecular evolutionary and synthetic biology experimental studies.

Mathematical and Computational Modelling of Ribosomal Movement and Protein Synthesis: an overview

Translation or protein synthesis consists of a complex system of chemical reactions, which ultimately result in decoding of the mRNA and the production of a protein. The complexity of this reaction system makes it difficult to quantitatively connect its input parameters (such as translation factor or ribosome concentrations, codon composition of the mRNA, or energy availability) to output parameters (such as protein synthesis rates or ribosome densities on mRNAs). Mathematical and computational models of translation have now been used for nearly five decades to investigate translation, and to shed light on the relationship between the different reactions in the system. This review gives an overview over the principal approaches used in the modelling efforts, and summarises some of the major findings that were made.

Smoothly varying hopping rates in driven flow with exclusion

We consider the one-dimensional totally asymmetric simple exclusion process (TASEP) with position-dependent hopping rates. The problem is solved, in a mean-field adiabatic approximation, for a general (smooth) form of spatial rate variation. Numerical simulations of systems with hopping rates varying linearly against position (constant rate gradient), for both periodic and open-boundary conditions, provide detailed confirmation of theoretical predictions, concerning steady-state average density profiles and currents, as well as open-system phase boundaries, to excellent numerical accuracy.

Incorporating friction and collective shear moves into a lattice gas

Here we examine a lattice-gas model that has been extended to include collective shear moves and friction interactions between particles. A shearlike field is applied by periodically translating entire subsections of the lattice with respect to one another, as opposed to biasing the individual movements of particles. Friction is introduced by forming a network of temporary bonds between particles that prevent particles from moving along with the flow. The extent of the network is controlled by the sticking parameter, P stk. We find that there are two distinct phases in the model: an isotropic phase that exhibits only small fluctuations in local density, and a striped phase that features one or more large clusters of particles that span the system. We examine the transition between these two phases using the radial distribution function. By introducing a measure of viscosity, we examine the relationship between the viscosity and shear rate for many different densities and values of P stk, and pursue an analogy to colloidal shear-thickening systems.

Comment on "Steady-state properties of a totally asymmetric exclusion process with periodic structure"

Lakatos et al.[Phys. Rev. E 71, 011103 (2005)] have studied a totally asymmetric exclusion process that contains periodically varying movement rates. They have presented a cluster mean-field theory for the problem. We show that their cluster mean-field theory leads to redundant equations. We present a mean-field analysis in which there is no redundant equation.

Traffic of interacting ribosomes: effects of single-machine mechanochemistry on protein synthesis

Many ribosomes simultaneously move on the same messenger RNA (mRNA), each synthesizing separately a copy of the same protein. In contrast to the earlier models, here we develop a "unified" theoretical model that not only incorporates the mutual exclusions of the interacting ribosomes, but also describes explicitly the mechanochemistry of each of these macromolecular machines during protein synthesis. Using analytical and numerical techniques of nonequilibrium statistical mechanics, we analyze the rates of protein synthesis and the spatiotemporal organization of the ribosomes in this model. We also predict how these properties would change with the changes in the rates of the various chemomechanical processes in each ribosome. Finally, we illustrate the power of this model by making experimentally testable predictions on the rates of protein synthesis and the density profiles of the ribosomes on some mRNAs in E-coli.

Characteristics of the asymmetric simple exclusion process in the presence of quenched spatial disorder

We investigate the effect of quenched spatial disordered hopping rates on the characteristics of the asymmetric simple exclusion process with open boundaries both numerically and by extensive simulations. Disorder averages of the bulk density and current are obtained in terms of various input and output rates. We study the binary and uniform distributions of disorder. It is verified that the effect of spatial inhomogeneity is generically to enlarge the size of the maximal-current phase. This is in accordance with the mean-field results obtained by Harris and Stinchcombe [Phys. Rev. E 70, 016108 (2004)]. Furthermore, we obtain the dependence of the current and the bulk density on the characteristics of the disorder distribution function. It is shown that the impact of disorder crucially depends on the particle input and out rates. In some situations, disorder can constructively enhance the current.