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Understanding totally asymmetric simple-exclusion-process transport on networks: Generic analysis via effective rates and explicit vertices 
Auteur(s): Embley Ben, Parmeggiani A., Kern N.
(Article) Publié:
Physical Review E: Statistical, Nonlinear, And Soft Matter Physics, vol. p.041128 (2009)
Ref HAL: hal-00504393_v1
Exporter : BibTex | endNote
Résumé: In this paper we rationalize relevant features of totally asymmetric simple exclusion processes on topologies more complex than a single segment. We present a mean-field framework, exploiting the previously introduced notion of effective rates, which we express in terms of the average particle density on explicitly introduced junction sites. It allows us to construct the phase behavior as well as the current-density characteristic from well-known results for a linear totally asymmetric simple-exclusion-process segment in a very systematic and generic way. We validate the approach by studying a fourfold vertex in all variations in the number of entering/exiting segments and compare our predictions to simulation data. Generalizing the notion of particle–hole symmetry to take into account the topology at a junction shows that the average particle density at the junction constitutes a relevant directly observable parameter which gives detailed insight into the transport process. This is illustrated by a complete study of a simple network with figure-of-eight topology. Finally we generalize the approach to handle rate bias at a junction and discuss the surprisingly rich phenomenology of a biased figure-of-eight structure. This example highlights that the proposed framework is generic and readily extends to other topologies.
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Tubulin and Microtubule Study under Hydrostatic Pressure
Auteur(s): Monnier Sylvain, Parmeggiani A., Larroque C., Lorman V.
Conference: PhysCell2009 (Primosten, HR, 2009-09-06)
Actes de conférence: Proceedings of PhysCell2009, Physics of Cells: From the Edge to the Heart, vol. p.p.149 (2009)
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Tubular Liquid Membrane Instabilities and Protein Coupling Mediated by Critical Modes
Auteur(s): Monnier Sylvain, Rochal S.B., Lorman V., Parmeggiani A.
Conference: PhysCell2009 (Primosten, HR, 2009-09-06)
Actes de conférence: Proceedings of PhysCell2009, Physics of Cells: From the Edge to the Heart, vol. p.p.54 (2009)
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Hex-Tasep : Dynamics of Pinned Domains for Tasep transport on a Periodic Lattice of Hexagonal Topology
Auteur(s): Embley Ben, Parmeggiani A., Kern N.
(Article) Publié:
Journal Of Physics: Condensed Matter, vol. 20 p.295213 (2008)
Ref HAL: hal-00504391_v1
DOI: 10.1088/0953-8984/20/29/295213
WoS: 000257325900033
Exporter : BibTex | endNote
12 Citations
Résumé: We investigate a totally asymmetric simple exclusion process (TASEP) on a periodic hexagonal lattice with a single unit cell. We first explain the resulting stationary density profiles and the resulting fundamental current–density relation in terms of mean-field arguments. For intermediate overall densities, transport through one of the segments saturates in a maximum current phase, whereas the others develop domain walls of fixed height but fluctuating position. Via kinetic Monte Carlo simulations we focus on and fully characterize their non-equilibrium and stochastic phenomenology. We invoke a picture of anticorrelated domain wall dynamics, which we visualize as a diffusing obstruction of constant size (‘jam'). The role of the boundary conditions is discussed by comparing the periodic lattice carrying a fixed number of particles to a system coupled to reservoirs at open boundaries which is periodic only on average. We highlight the differences in their dynamics based on a novel visualization of domain wall motion at an intermediate ‘mesoscopic' timescale.
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Tubulin and Microtubule Study under Hydrostatic Pressure
Auteur(s): Monnier Sylvain, Estephan E., Marchal S., Lange R., Bec N., Larroque C., Lorman V., Parmeggiani A.
Conference: HPMB2008 (Synchrotron SOLEIL, Saint Aubin (Gif-sur-Yvette), FR, 2008-12-10)
Actes de conférence: Proceedings of the International Conference on High-Pressure Molecular Biophysics, vol. p.- (2008)
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Tubulin and Microtubule Study under Hydrostatic Pressure
Auteur(s): Monnier Sylvain, Estephan E., Parmeggiani A., Marchal S., Lange R., Bec N., Lorman V.
Conference: From Solid State to Biophysics IV (Cavtat, Dubrovnik, HR, 2008-06-06)
Actes de conférence: Proceedings of the 4th International Conference"From Solid State to Biophysics IV", vol. p.C-78 (2008)
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Dynamics of topological TASEP, Biophysics and Microfluides
Auteur(s): Kern N., Embley Ben, Parmeggiani A.
(Affiches/Poster)
Biarritz (Biarritz, FR), 2007-10-07 |
