Ref HAL: tel-01930091_v1
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Résumé:

Résumé de mon travail de recherche et de l'encadrement de la recherche : simulations du comportement de phases de protéines, structure et écoulement de mousses de savon, transport stochastique

Résumé:

The Totally Asymmetric Simple Exclusion Process is a minimal model for 1d out-of-equilibrium transport, which is not only relevant to fundamental physics but also to many applications. It is useful for modelling the action of ribosomes during transcription, but can also be applied to describe molecular motors as they transport cargos along the bio-filaments. With a view to ultimately modelling processes relevant to cytoskeletal transport, we explore here simple scenarios for networks, and in particular for their topology. The junctions interconnecting the filaments turn out to play a crucial role, both for understanding transport on a network as well as for controlling it.

Ref HAL: hal-01935611_v1
DOI: 10.1007/978-4-431-54907-9_1
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Biological cells require active fluxes of matter to maintain their internal organization and perform multiple tasks to live. In particular they rely on cytoskeletal transport driven by motor proteins, ATP-fueled molecular engines, for delivering vesicles and biochemically active cargoes inside the cytoplasm. Experimental progress allows nowadays quantitative studies describing intracellular transport phenomena down to the nanometric scale of single molecules. Theoretical approaches face the challenge of modelling the multiscale, out-of-equilibrium and non-linear properties of cytoskeletal transport: from the mechanochemical complexity of a single molecular motor up to the collective transport on cellular scales. We will present some of our recent progress in building a generic modelling scheme for cytoskeletal transport based on lattice gas models called “exclusion processes”. Interesting new properties arise from the emergence of density inhomogeneities of particles along the network of one dimensional lattices. Moreover, understanding these processes on networks can provide important hints for other fundamental and applied problems such as vehicular, pedestrian and data traffic, or ultimately for technological and biomedical applications.

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-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.