Domaines de Recherche:  Sciences du Vivant/Biologie cellulaire/Organisation et fonctions cellulaires [qbio.SC]
 Physique/Matière Condensée/Mécanique statistique
 Physique/Physique/Biophysique
 Science non linéaire/Automates cellulaires et gaz sur réseau [nlin.CG]
 Physique/Matière Condensée/Systèmes désordonnés et réseaux de neurones

Dernieres productions scientifiques :


Motor proteins traffic regulation by supplydemand balance of resources
Auteur(s): Ciandrini L., Neri I., Walter J.C., Dauloudet O., Parmeggiani A.
(Article) Publié:
Physical Biology, vol. 11 p.056006 (2014)
Ref HAL: hal01063014_v1
Ref Arxiv: 1408.2945
DOI: 10.1088/14783975/11/5/056006
Ref. & Cit.: NASA ADS
Exporter : BibTex  endNote
Résumé: In cells and in vitro assays the number of motor proteins involved in biological transport processes is far from being unlimited. The cytoskeletal binding sites are in contact with the same finite reservoir of motors (either the cytosol or the flow chamber) and hence compete for recruiting the available motors, potentially depleting the reservoir and affecting cytoskeletal transport. In this work we provide a theoretical framework to study, analytically and numerically, how motor density profiles and crowding along cytoskeletal filaments depend on the competition of motors for their binding sites. We propose two models in which finite processive motor proteins actively advance along cytoskeletal filaments and are continuously exchanged with the motor pool. We first look at homogeneous reservoirs and then examine the effects of free motor diffusion in the surrounding medium. We consider as a reference situation recent in vitro experimental setups of kinesin8 motors binding and moving along microtubule filaments in a flow chamber. We investigate how the crowding of linear motor proteins moving on a filament can be regulated by the balance between supply (concentration of motor proteins in the flow chamber) and demand (total number of polymerised tubulin heterodimers). We present analytical results for the density profiles of bound motors, the reservoir depletion, and propose novel phase diagrams that present the formation of jams of motor proteins on the filament as a function of two tuneable experimental parameters: the motor protein concentration and the concentration of tubulins polymerized into cytoskeletal filaments. Extensive numerical simulations corroborate the analytical results for parameters in the experimental range and also address the effects of diffusion of motor proteins in the reservoir.
Commentaires: 31 pages, 10 figures



Exclusion processes on networks as models for cytoskeletal transport
Auteur(s): Neri I., Kern N., Parmeggiani A.
(Article) Publié:
New Journal Of Physics, vol. 15 p.085005 (2013)
Ref HAL: hal00904086_v1
Ref Arxiv: 1304.1943
DOI: 10.1088/13672630/15/8/085005
Ref. & Cit.: NASA ADS
Exporter : BibTex  endNote
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 multiscale factors, such as the interplay of exclusion interactions, the nonequilibrium 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 nonequilibrium 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 bidirectional motion along a network or infinite diffusion) and outofequilibrium 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



Modeling Cytoskeletal Traffic: An Interplay between Passive Diffusion and Active Transport
Auteur(s): Neri I., Kern N., Parmeggiani A.
(Article) Publié:
Physical Review Letters, vol. 110 p.098102 (2013)
Ref HAL: hal00805162_v1
DOI: 10.1103/PhysRevLett.110.098102
Exporter : BibTex  endNote
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 singlesegment phase diagram.



Characterising stationary states in exclusion processes on networks
Auteur(s): Kern N., Parmeggiani A., Neri I.
Conférence invité: Characterising stationary states in exclusion processes on networks (MMontpellier, FR, 20130325)
Ref HAL: hal00805148_v1
Exporter : BibTex  endNote
Résumé: 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, socalled '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.



Towards modelling motor protein driven cytoskeltal transport
Auteur(s): Kern N., Parmeggiani A., Raguin A., Neri I.
Conference: Mechanisms driving the organization of intracellular organelles (Zaragoza, ES, 20120618)
Résumé: One important role which the cytoskeleton plays in cells is to provide a network of filaments along which molecular motors can procede. This provides an essential mechanism by which a cell can establish transport of cargos over distances of the order of the cell size. The details of how such motors achieve procession along the biofilaments constituting the cytoskeleton are very complex indeed, but much of their behaviour (including collective aspects of the transport) can be described in terms of wellestablished models, such as the Totally Asymmetric Transport Process (TASEP) or similar. These are wellstudied on single filaments. Recent work has allowed us to establish a framework to transpose this understanding to an overall network of interconnected filaments, mimicking the cytoskeleton. We discuss how new aspects of heterogeneity arise on the network scale, and we aOne important role which the cytoskeleton plays in cells is to provide a network of filaments along which molecular motors can procede. This provides an essential mechanism by which a cell can establish transport of cargos over distances of the order of the cell size. The details of how such motors achieve procession along the biofilaments constituting the cytoskeleton are very complex indeed, but much of their behaviour (including collective aspects of the transport) can be described in terms of wellestablished models, such as the Totally Asymmetric Transport Process (TASEP) or similar. These are wellstudied on single filaments. Recent work has allowed us to establish a framework to transpose this understanding to an overall network of interconnected filaments, mimicking the cytoskeleton. We discuss how new aspects of heterogeneity arise on the network scale, and we argue that they are generic to many types of transport on networks. We also present very recent ideas for incorporating more complex features aimed at applying the approach to cytoskeletal transport in particular.
rgue that they are generic to many types of transport on networks. We also present very recent ideas for incorporating more complex features aimed at applying the approach to cytoskeletal transport in particular.

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