Ref HAL: hal-01531052_v1
DOI: 10.1103/PhysRevE.88.042104
WoS: WOS:000325167500004
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14 Citations
Résumé:

We study the effect of local regulation mechanisms on stochastic network traffic, based on simple examples. Using the totally asymmetric simple exclusion process on a multiloop structure in which several segments share a single junction, we illustrate several mechanisms: (i) additional segments improve transport but the effect saturates due to blockage, (ii) bias reduces the overall transport and leads to several regimes, (iii) “pumping” particles out of the junctions, via a locally increased hopping rate, allows us to compensate the bottlenecks but becomes futile beyond a characteristic rate which we determine. We provide a generic discussion of combinations of these effects, including phase diagrams in terms of the control parameters.

Ref HAL: hal-00904086_v1
Ref Arxiv: 1304.1943
DOI: 10.1088/1367-2630/15/8/085005
WoS: 000322953600002
Ref. & Cit.: NASA ADS
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54 Citations
Résumé:

We present a study of exclusion processes on networks as models for complex transport phenomena and in particular for active transport of motor proteins along the cytoskeleton. We argue that active transport processes on networks spontaneously develop density heterogeneities at various scales. These heterogeneities can be regulated through a variety of multi-scale factors, such as the interplay of exclusion interactions, the non-equilibrium nature of the transport process and the network topology. We show how an effective rate approach allows to develop an understanding of the stationary state of transport processes through complex networks from the phase diagram of one single segment. For exclusion processes we rationalize that the stationary state can be classified in three qualitatively different regimes: a homogeneous phase as well as inhomogeneous network and segment phases. In particular, we present here a study of the stationary state on networks of three paradigmatic models from non-equilibrium statistical physics: the totally asymmetric simple exclusion process, the partially asymmetric simple exclusion process and the totally asymmetric simple exclusion process with Langmuir kinetics. With these models we can interpolate between equilibrium (due to bi-directional motion along a network or infinite diffusion) and out-of-equilibrium active directed motion along a network. The study of these models sheds further light on the emergence of density heterogeneities in active phenomena.

Commentaires: 55 pages, 26 figures Journal: New J. Phys. 15 (2013) 085005

Ref HAL: hal-00816492_v1
PMID 23410357
DOI: 10.1103/PhysRevE.87.012705
WoS: 000314150800002
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24 Citations
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Many transport processes in nature take place on substrates, often considered as unidimensional lanes. These unidimensional substrates are typically nonstatic: Affected by a fluctuating environment, they can undergo conformational changes. This is particularly true in biological cells, where the state of the substrate is often coupled to the active motion of macromolecular complexes, such as motor proteins on microtubules or ribosomes on mRNAs, causing new interesting phenomena. Inspired by biological processes such as protein synthesis by ribosomes and motor protein transport, we introduce the concept of localized dynamical sites coupled to a driven lattice gas dynamics. We investigate the phenomenology of transport in the presence of dynamical defects and find a regime characterized by an intermittent current and subject to severe finite-size effects. Our results demonstrate the impact of the regulatory role of the dynamical defects in transport not only in biology but also in more general contexts. DOI: 10.1103/PhysRevE.87.012705

Ref HAL: inserm-00749959_v1
PMID 23047900
DOI: 10.1096/fj.11-202465
WoS: 000313103200012
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7 Citations
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The nonreceptor Syk kinase is detected in epithelial cells, where it acts as a tumor suppressor, in addition to its well-established role in immunoreceptor-based signal transduction in hematopoietic cells. Thus, several carcinomas and melanomas have subnormal concentrations of Syk. Although Syk is mainly localized at the plasma membrane, it is also present in centrosomes, where it is involved in the control of cell division. The mechanisms responsible for its centrosomal localization and action are unknown. We used wild-type and mutant fluorescent Syk fusion proteins in live-cell imaging (fluorescence recovery after photobleaching, total internal reflection fluorescence, and photoactivation) combined with mathematical modeling to demonstrate that Syk is actively transported to the centrosomes via the microtubules and that this transport depends on the dynein/dynactin molecular motor. Syk can only target the centrosomes if its kinase activity is intact and it is catalytically active at the centrosomes. We showed that the autophosphorylated Y130 Syk residue helps to uncouple Syk from the plasma membrane and to promote its translocation to the centrosome, suggesting that the subcellular location of Syk depends on its autophosphorylation on specific tyrosine residues. We have thus established the details of how Syk is trafficked intracellularly and found evidence that its targeting to the centrosomes is controlled by autophosphorylation.

Ref HAL: hal-00816496_v1
DOI: 10.1103/Physics.5.118
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Few mathematical tools exist for describing non-equilibrium systems, but new methods may emerge from the study of a simple transport model.

Ref HAL: hal-00805162_v1
DOI: 10.1103/PhysRevLett.110.098102
WoS: 000315488300017
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57 Citations
Résumé:

We introduce the totally asymmetric simple exclusion process with Langmuir kinetics on a network as a microscopic model for active motor protein transport on the cytoskeleton, immersed in the diffusive cytoplasm.We discuss how the interplay between active transport along a network and infinite diffusion in a bulk reservoir leads to a heterogeneous matter distribution on various scales: we find three regimes for steady state transport, corresponding to the scale of the network, of individual segments, or local to sites. At low exchange rates strong density heterogeneities develop between different segments in the network. In this regime one has to consider the topological complexity of the whole network to describe transport. In contrast, at moderate exchange rates the transport through the network decouples, and the physics is determined by single segments and the local topology. At last, for very high exchange rates the homogeneous Langmuir process dominates the stationary state. We introduce effective rate diagrams for the network to identify these different regimes. Based on this method we develop an intuitive but generic picture of how the stationary state of excluded volume processes on complex networks can be understood in terms of the single-segment phase diagram.

Ref HAL: hal-00805148_v1
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The notion of networks arises naturally in many problems: transmission of information, road networks, cytoskeletal transport and gene regulation are timely examples. It is often useful to envisage two complementary aspects defining these systems, rules for transmission/propagation on one hand and network topology on the other hand. We generalise a simple class of models, so-called 'exclusion processes', to networks. We outline how to solve for stationary states and provide a method to characterise these stationary states in a simple but quantifiable way. Such 'effective rate plots' will be seen to prove particularly useful for gaining intuition on the essence of these states and on the effect of the network structure.