Sample-dependent phase transitions in disordered exclusion models

Enaud, C.; Derrida, Bernard

doi:10.1209/epl/i2003-10153-8

Cited by 45 publications

(37 citation statements)

References 36 publications

(60 reference statements)

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“…a macroscopic number of slow bonds. Here previous investigations for periodic [25][26][27][28] and open systems [28][29][30][31][32][33] have revealed surprising results. For the open system, for example, it has been found [30] that the position of the phase transitions is sensitively sample-dependent even for large systems.…”

Section: Introductionmentioning

confidence: 76%

Phase diagram and edge effects in the ASEP with bottlenecks

Greulich

Schadschneider

2008

Physica A: Statistical Mechanics and its Applications

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We investigate the totally asymmetric simple exclusion process (TASEP) in the presence of a bottleneck, i.e. a sequence of consecutive defect sites with reduced hopping rate. The influence of such a bottleneck on the phase diagram is studied by computer simulations and a novel analytical approach. We find a clear dependence of the current and the properties of the phase diagram not only on the length of the bottleneck, but also on its position. For bottlenecks near the boundaries, this motivates the concept of effective boundary rates. Furthermore the inclusion of a second, smaller bottleneck far from the first one has no influence on the transport capacity. These results will form the basis of an effective description of the disordered TASEP and are relevant for the modelling of protein synthesis or intracellular transport systems where the motion of molecular motors is hindered by immobile blocking molecules.Comment: accepted by Physica

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Section: Introductionmentioning

confidence: 76%

Phase diagram and edge effects in the ASEP with bottlenecks

Greulich

Schadschneider

2008

Physica A: Statistical Mechanics and its Applications

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“…Sequence inhomogeneity can lead to site-dependent rates of translocation of RNAP on its track. In the context of TASEP, which is a special limit of our model of RNAP traffic, effects of quenched random site-dependent hopping rates [59,60,61,62,63,64,65,66,67], have been investigated extensively over the last decade. Moreover, Brownian motors with quenched disorder [68,69,70,71] have also been studied.…”

Section: B Brief Review Of the Earlier Modelsmentioning

confidence: 99%

Interacting RNA polymerase motors on a DNA track: Effects of traffic congestion and intrinsic noise on RNA synthesis

Tripathi

Chowdhury

2008

Phys. Rev. E

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RNA polymerase (RNAP) is an enzyme that synthesizes a messenger RNA (mRNA) strand which is complementary to a single-stranded DNA template. From the perspective of physicists, an RNAP is a molecular motor that utilizes chemical energy input to move along the track formed by a DNA. In many circumstances, which are described in this paper, a large number of RNAPs move simultaneously along the same track; we refer to such collective movements of the RNAPs as RNAP traffic. Here we develop a theoretical model for RNAP traffic by incorporating the steric interactions between RNAPs as well as the mechano-chemical cycle of individual RNAPs during the elongation of the mRNA. By a combination of analytical and numerical techniques, we calculate the rates of mRNA synthesis and the average density profile of the RNAPs on the DNA track. We also introduce, and compute, two new measures of fluctuations in the synthesis of RNA. Analyzing these fluctuations, we show how the level of intrinsic noise in mRNA synthesis depends on the concentrations of the RNAPs as well as on those of some of the reactants and the products of the enzymatic reactions catalyzed by RNAP. We suggest appropriate experimental systems and techniques for testing our theoretical predictions.

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“…Notwithstanding the simplicity of formulation of its basic rules, this model can exhibit a wealth of non-trivial properties, and is considered a paradigm in the field of non-equilibrium phenomena. Quenched random inhomogeneities in the TASEP have been extensively considered earlier [5][6][7][8][9][10][11][12]. In contrast, the case of deterministically-varying, positiondependent physical parameters has received less attention [13,14].…”

Section: Introductionmentioning

confidence: 99%

Smoothly varying hopping rates in driven flow with exclusion

Stinchcombe

Queiroz

2011

Phys. Rev. E

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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 steadystate average density profiles and currents, as well as open-system phase boundaries, to excellent numerical accuracy.

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Sample-dependent phase transitions in disordered exclusion models

Cited by 45 publications

References 36 publications

Phase diagram and edge effects in the ASEP with bottlenecks

Phase diagram and edge effects in the ASEP with bottlenecks

Interacting RNA polymerase motors on a DNA track: Effects of traffic congestion and intrinsic noise on RNA synthesis

Smoothly varying hopping rates in driven flow with exclusion

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