Stochastic models of intracellular transport

Bressloff, Paul C.; Newby, Jay M.

doi:10.1103/revmodphys.85.135

Cited by 588 publications

(607 citation statements)

References 395 publications

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“…Several modelling approaches can be pursued to model cytoskeletal motors [56]. We shall now review a few of them and discuss their domain of applicability.…”

Section: Motor Modellingmentioning

confidence: 99%

Intracellular transport driven by cytoskeletal motors: General mechanisms and defects

2015

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Cells are the elementary units of living organisms, which are able to carry out many vital functions. These functions rely on active processes on a microscopic scale. Therefore, they are strongly out-of-equilibrium systems, which are driven by continuous energy supply. The tasks that have to be performed in order to maintain the cell alive require transportation of various ingredients, some being small, others being large. Intracellular transport processes are able to induce concentration gradients and to carry objects to specific targets. These processes cannot be carried out only by diffusion, as cells may be crowded, and quite elongated on molecular scales. Therefore active transport has to be organized.The cytoskeleton, which is composed of three types of filaments (microtubules, actin and intermediate filaments), determines the shape of the cell, and plays a role in cell motion. It also serves as a road network for a special kind of vehicles, namely the cytoskeletal motors. These molecules can attach to a cytoskeletal filament, perform directed motion, possibly carrying along some cargo, and then detach.It is a central issue to understand how intracellular transport driven by molecular motors is regulated. The interest for this type of question was enhanced when it was discovered that intracellular transport breakdown is one of the signatures of some neuronal diseases like the Alzheimer.We give a survey of the current knowledge on microtubule based intracellular transport. Our review includes on the one hand an overview of biological facts, obtained from experiments, and on the other hand a presentation of some modeling attempts based on cellular automata. We present some background knowledge on the original and variants of the TASEP (Totally Asymmetric Simple Exclusion Process), before turning to more application oriented models. After addressing microtubule based transport in general, with a focus on in vitro experiments, and on cooperative effects in the transportation of large cargos by multiple motors, we concentrate on axonal transport, because of its relevance for neuronal diseases. Some important characteristics of axonal transport is that it takes place in a confined environment; Besides several types of motors are involved, that move in opposite directions. It is a challenge to understand how this bidirectional transport is organized. We review several features that could contribute to the efficiency of bidirectional transport in the axon, including in particular the role of motor-motor interactions and of the dynamics of the underlying microtubule network. Finally, we also discuss some open questions that may be relevant for future research in this field.

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“…Several modelling approaches can be pursued to model cytoskeletal motors [56]. We shall now review a few of them and discuss their domain of applicability.…”

Section: Motor Modellingmentioning

confidence: 99%

Intracellular transport driven by cytoskeletal motors: General mechanisms and defects

2015

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“…This has led to many interesting collective effects in models of elastically coupled motors [15,16,17,1,3,4] and excluded volume interactions [18,19,20,21,22,23,24,25,26,27,28,29]. Of particular interest to the present work is the model of a discrete flashing ratchet considered in [30,31] in which large scale properties of a system of hard-core particles moving in a ratchet potential defined on a discrete lattice was studied.…”

Section: Introductionmentioning

confidence: 99%

“…Flashing Ratchets are an extensively studied class of systems in which a combination of thermal noise, a periodic asymmetric potential and an external forcing which breaks detailed balance, results in a net directional flux [1,2]. These have become very relevant as models of active directed transport in intracellular processes as they offer a natural mechanism for maintaining global currents in the absence of a global driving field [3,4]. The ratchet mechanism has found practical applications in areas of controlling particle motion at nano scale [5,6], from microfluidics to nanoscale machines [7] and controlling motion of magnetic flux quanta in superconductors [8,9,10,11,12,13,14] .…”

Section: Introductionmentioning

confidence: 99%

Interacting particles in disordered flashing ratchets

Chacko

Tripathy

2015

Indian J Phys

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We study the steady state properties of a system of particles interacting via hard core exclusion and moving in a discrete flashing disordered ratchet potential. Quenched disorder is introduced by breaking the periodicity of the ratchet potential through changing shape of the potential across randomly chosen but fixed periods. We show that the effects of quenched disorder can be broadly classified as strong or weak with qualitatively different behaviour of the steady state particle flux as a function of overall particle density. We further show that most of the effects including a density driven nonequilibrium phase transition observed can be understood by constructing an effective asymmetric simple exclusion process (ASEP) with quenched disorder in the hop rates.

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“…In terms of motion in continuous space, the interplay between stepping strategy and persistency of the walker is established as a source of anomalous diffusion at short and intermediate time scales. Anomalous transport of self-propelled particles in biological environments has received much recent attention [1]. Of particular interest is the active motion of motor proteins along cytoskeletal filaments, which makes longdistance intracellular transport feasible [2].…”

mentioning

confidence: 99%

“…Ka, 87.16.Uv, 87.16.Nn Anomalous transport of self-propelled particles in biological environments has received much recent attention [1]. Of particular interest is the active motion of motor proteins along cytoskeletal filaments, which makes longdistance intracellular transport feasible [2].…”

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confidence: 99%

Anomalous diffusion of self-propelled particles in directed random environments

et al. 2014

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We theoretically study the transport properties of self-propelled particles on complex structures, such as motor proteins on filament networks. A general master equation formalism is developed to investigate the persistent motion of individual random walkers, which enables us to identify the contributions of key parameters: the motor processivity, and the anisotropy and heterogeneity of the underlying network. We prove the existence of different dynamical regimes of anomalous motion, and that the crossover times between these regimes as well as the asymptotic diffusion coefficient can be increased by several orders of magnitude within biologically relevant control parameter ranges. In terms of motion in continuous space, the interplay between stepping strategy and persistency of the walker is established as a source of anomalous diffusion at short and intermediate time scales.PACS numbers: 87.16. Ka, 87.16.Uv, 87.16.Nn Anomalous transport of self-propelled particles in biological environments has received much recent attention [1]. Of particular interest is the active motion of motor proteins along cytoskeletal filaments, which makes longdistance intracellular transport feasible [2]. The structural asymmetry of filaments results in a directed motion of motors with an effective processivity, denoting the tendency to move along the same filament. The processivity depends on the type of motor and filament [3] and it is strongly influenced by the presence of specific proteins or binding domains [4,5]. In the limit of small unbinding rates it has been shown [6] that a walker on simple lattice structures moves superdiffusively at short time scales followed by a normal diffusion at long times. Similar results were reported for single bead motion on radiallyorganized microtubule networks [7]. However, for general polarized cytoskeletal networks, the influence of structural complexity and motor processivity on the transport properties is not yet well understood. In this Rapid Communication, we introduce a coarse-grained perspective to the problem and show that the interplay between anisotropy and heterogeneity of the network and processivity leads to a rich transport phase diagram at short and intermediate time scales. The crossover times between different regimes and the asymptotic diffusion constant can vary by orders of magnitude when tuning the key parameters.More precisely, a general analytical framework is developed to study persistent walks with arbitrary steplength and turning-angle distributions. We obtain an exact analytical expression for the dynamical evolution of the mean square displacement (MSD), displaying anomalous diffusion on varying time scales. The results can be also interpreted within the context of random motion in continuous space, e.g. in crowded biological media where the origin of subdiffusive motion is highly debated [8][9][10][11][12][13].While subdiffusion in cytoplasm slows down the transfer of matter, it is beneficial for a variety of cellular functions [14-16], since they depend on th...

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Stochastic models of intracellular transport

Cited by 588 publications

References 395 publications

Intracellular transport driven by cytoskeletal motors: General mechanisms and defects

Intracellular transport driven by cytoskeletal motors: General mechanisms and defects

Interacting particles in disordered flashing ratchets

Anomalous diffusion of self-propelled particles in directed random environments

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