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DOI: 10.1140/epje/s10189-021-00061-6
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erratum

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Ref Arxiv: 2009.14533
DOI: 10.1140/epje/s10189-021-00019-8
Ref. & Cit.: NASA ADS
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Translation is one of the main steps in the synthesis of proteins. It consists of ribosomes that translate sequences of nucleotides encoded on mRNA into polypeptide sequences of amino acids. Ribosomes bound to mRNA move unidirectionally, while unbound ribosomes diffuse in the cytoplasm. It has been hypothesized that finite diffusion of ribosomes plays an important role in ribosome recycling and that mRNA circularization enhances the efficiency of translation. In order to estimate the effect of cytoplasmic diffusion on the rate of translation, we consider a Totally Asymmetric Simple Exclusion Process (TASEP) coupled to a finite diffusive reservoir, which we call the Ribosome Transport model with Diffusion (RTD). In this model, we derive an analytical expression for the rate of protein synthesis as a function of the diffusion constant of ribosomes, which is corroborated with results from continuous-time Monte Carlo simulations. Using a wide range of biological relevant parameters, we conclude that diffusion in biological cells is fast enough so that it does not play a role in controlling the rate of translation initiation.

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.

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PMID 25204752
Ref Arxiv: 1408.2945
DOI: 10.1088/1478-3975/11/5/056006
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22 Citations
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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 kinesin-8 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

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Ref Arxiv: 1304.1943
DOI: 10.1088/1367-2630/15/8/085005
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54 Citations
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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

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DOI: 10.1103/PhysRevLett.110.098102
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57 Citations
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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.