Transport properties in disordered ratchet potentials

Marchesoni, F.

doi:10.1103/physreve.56.2492

Cited by 54 publications

(25 citation statements)

References 19 publications

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“…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. In the same spirit, single molecular motors, which move on DNA or RNA tracks, have been modelled assuming the nucleotide sequence on the track to be random [72,73].…”

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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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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“…Introduction.-A number of authors (see, e.g., [1][2][3][4]) have recently addressed the longstanding problem of how to extract useful work from a fluctuating environment. While heat may not be transformed back to mechanical work at thermal equilibrium (i.e., without temperature gradients [5]), the same restriction does not apply to the case of nonequilibrium thermal fluctuations: An asymmetric device (like Feynman's ratchet [5]) can indeed rectify symmetric quasi-equilibrium fluctuations [1][2][3][4]. The implications of such a mechanism in transport theory are far-reaching: macroscopic currents may arise even in the absence of external forces or gradients.…”

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confidence: 99%

Superconducting Fluxon Pumps and Lenses

et al. 1999

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We study stochastic transport of fluxons in superconductors by alternating current (AC) rectification. Our simulated system provides a fluxon pump, "lens", or fluxon "rectifier" because the applied electrical AC is transformed into a net DC motion of fluxons. Thermal fluctuations and the asymmetry of the ratchet channel walls induce this "diode" effect, which can have important applications in devices, like SQUID magnetometers, and for fluxon optics, including convex and concave fluxon lenses. Certain features are unique to this novel two-dimensional (2D) geometric pump, and different from the previously studied 1D ratchets.Comment: Phys. Rev. Lett. 83, in press (1999); 4 pages, 5 .gif figures; figures also available at http://www-personal.engin.umich.edu/~nori/ratche

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“…a perturbation of the thermal motion of a Brownian particle that results in its directed transport with a bias in a preferred direction, can be easily achieved by introducing a spatial or dynamical asymmetry in the system [42,43], but it could be quenched by the presence of excessive disorder [44]. In our experiment, repeating the previous cycle as shown in Fig.…”

Section: Resultsmentioning

confidence: 89%

Speckle optical tweezers: micromanipulation with random light fields

Volpe¹,

Kurz²,

Callegari³

et al. 2014

Opt. Express

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Current optical manipulation techniques rely on carefully engineered setups and samples. Although similar conditions are routinely met in research laboratories, it is still a challenge to manipulate microparticles when the environment is not well controlled and known a priori, since optical imperfections and scattering limit the applicability of this technique to real-life situations, such as in biomedical or microfluidic applications. Nonetheless, scattering of coherent light by disordered structures gives rise to speckles, random diffraction patterns with welldefined statistical properties. Here, we experimentally demonstrate how speckle fields can become a versatile tool to efficiently perform fundamental optical manipulation tasks such as trapping, guiding and sorting. We anticipate that the simplicity of these "speckle optical tweezers" will greatly broaden the perspectives of optical manipulation for real-life applications.

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Transport properties in disordered ratchet potentials

Cited by 54 publications

References 19 publications

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

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

Superconducting Fluxon Pumps and Lenses

Speckle optical tweezers: micromanipulation with random light fields

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