Inhomogeneous exclusion processes with extended objects: The effect of defect locations

Abstract

We study the effects of local inhomogeneities, i.e., slow sites of hopping rate $q<1$, in a totally asymmetric simple exclusion process (TASEP) for particles of size $\ell \ge 1$ (in units of the lattice spacing). We compare the simulation results of $\ell =1$ and $\ell >1$ and notice that the existence of local defects has qualitatively similar effects on the steady state. We focus on the stationary current as well as the density profiles. If there is only a single slow site in the system, we observe a significant dependence of the current on the \emph{location} of the slow site for both $\ell =1$ and $\ell >1$ cases. When two slow sites are introduced, more intriguing phenomena emerge, e.g., dramatic decreases in the current when the two are close together. In addition, we study the asymptotic behavior when $q\to 0$. We also explore the associated density profiles and compare our findings to an earlier study using a simple mean-field theory. We then outline the biological significance of these effects.

14 pages; 14 figures

References in corpus (16)

• Phase transitions in an exactly soluble one-dimensional exclusion process
• The totally asymmetric exclusion process with extended objects, a model for protein synthesis
• Bethe Ansatz Solution of the Asymmetric Exclusion Process with Open Boundaries
• Clustered bottlenecks in mRNA translation and protein synthesis
• Exact Results for the Asymmetric Simple Exclusion Process with a Blockage
• Phase separation in disordered exclusion models
• Driven Lattice Gases with Quenched Disorder: Exact Results and Different Macroscopic Regimes
• Local Inhomogeneity in Asymmetric Simple Exclusion Processes with Extended Objects
• Disordered asymmetric simple exclusion process: mean-field treatment
• Towards a model for protein production rates
• Towards a model for protein production rates
• Queuing Transitions in the Asymmetric Simple Exclusion Process
• Exclusion process for particles of arbitrary extension: Hydrodynamic limit and algebraic properties
• Tagged Particle Correlations in the Asymmetric Simple Exclusion Process: Finite Size Effects
• The Exact Solution of the Asymmetric Exclusion Problem With Particles of Arbitrary Size: Matrix Product Ansatz
• Power Spectra of the Total Occupancy in the Totally Asymmetric Simple Exclusion Process

Cited by in corpus (35)

• Non-equilibrium statistical mechanics: From a paradigmatic model to biological transport
• Modeling Translation in Protein Synthesis with TASEP: A Tutorial and Recent Developments
• Mixed population of competing TASEPs with a shared reservoir of particles
• Role of the particle's stepping cycle in an asymmetric exclusion process: A model of mRNA translation
• Far-from-equilibrium transport with constrained resources
• Competition between Multiple Totally Asymmetric Simple Exclusion Processes for a Finite Pool of Resources
• Stochastic kinetics of ribosomes: single motor properties and collective behavior
• The key parameters that govern translation efficiency
• Feedback and Fluctuations in a Totally Asymmetric Simple Exclusion Process with Finite Resources
• Single-Bottleneck Approximation for Driven Lattice Gases with Disorder and Open Boundary Conditions
• Twenty five years after KLS: A celebration of non-equilibrium statistical mechanics
• Asymmetric Exclusion Processes with Disorder: Effect of Correlations
• Distribution of dwell times of a ribosome: effects of infidelity, kinetic proofreading and ribosome crowding
• Signal optimization in urban transport: A totally asymmetric simple exclusion process with traffic lights
• Entrainment and unit velocity: Surprises in an accelerated exclusion process
• Interplay between finite resources and local defect in an asymmetric simple exclusion process
• Driven k-mers: Correlations in space and time
• Dynamical phase transition of a 1D transport process including death
• Power Spectra of a Constrained Totally Asymmetric Simple Exclusion Process
• Understanding the edge effect in TASEP with mean-field theoretic approaches
• Current-density relation in the exclusion process with dynamic obstacles
• Competition for finite resources
• Interference of two co-directional exclusion processes in the presence of a static bottleneck: a biologically motivated model
• Phase separation transition of reconstituting k-mers in one dimension
• EGGTART: A computational tool to visualize the dynamics of biophysical transport processes under the inhomogeneous $\ell$-TASEP
• A Multispecies Exclusion Process with Fusion and Fission of Rods: a model inspired by Intraflagellar Transport
• Reservoir crowding in a totally asymmetric simple exclusion process with Langmuir Kinetics
• Defect versus defect: stationary states of single file marching in periodic landscapes with road blocks
• Phase coexistence and spatial correlations in reconstituting k-mer models
• Exclusion process subject to conformational size changes
• Simulations of driven and reconstituting lattice gases
• Power spectra of TASEPs with a localized slow site
• Analytical results for a coagulation/decoagulation model on an inhomogeneous lattice
• Ribosome Flow Model with Extended Objects
• On the Structure of the Initiation and Elongation Rates that Maximize Protein Production in the Ribosome Flow Model