Confined Brownian ratchets

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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“…Some complementary mechanisms, for example through hydrodynamic interactions, could also play a role in obtaining correlated motion [238,239].…”

Section: Tug-of-warmentioning

confidence: 99%

Intracellular transport driven by cytoskeletal motors: General mechanisms and defects

2015

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“…The staring point of our model is the Fick-Jacobs approximation [24][25][26] that has already been characterized [27][28][29][30][31][32][33] and exploited for diverse systems ranging from particle splitters [34,35], cooperative rectification [36][37][38] diffusion through porous media [39,40], electro-osmotic systems [41][42][43] and entropic stochastic resonance [44,45] just to mention a few cases among others. The Fick-Jacobs approximation allows us to project the convection-diffusion equation of a noninteracting particle, confined in a two-dimensional (2D) or three-dimensional (3D) corrugated channel, onto a one-dimensional (1D) equation in which the particle dynamics is controlled by an effective potential.…”

Section: Theoretical Framework a Fick-jacobs Approximationmentioning

confidence: 99%

Non-monotonous polymer translocation time across corrugated channels: Comparison between Fick-Jacobs approximation and numerical simulations

Bianco

Malgaretti

2016

The Journal of Chemical Physics

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We study the translocation of polymers across varying-section channels. Using systematic approximations, we derive a simplified model that reduces the problem of polymer translocation through varying-section channels to that of a point-like particle under the action of an effective potential. Such a model allows us to identify the relevant parameters controlling the polymers dynamics and, in particular, their translocation time. By comparing our analytical results with numerical simulations we show that, under suitable conditions, our model provides reliable predictions of the dynamics of both Gaussian and self-avoiding polymers, in two-and three-dimensional confinement. Moreover, both theoretical predictions, as well Brownian dynamic results, show a non-monotonous dependence of polymer translocation velocity as a function of polymer size, a feature that can be exploited for polymer separation.

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“…1 i.e. the dynamics of ions density is well captured by the concept of entropic barriers [21][22][23]. For ∂ x h(x) ≫ 1 the factorization in Eq.…”

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confidence: 99%

“…In order to characterize this electrokinetic transport regime, we will consider a symmetric, z −z electrolyte solution, in contact with a reservoir of ionic strength ρ 0 z 2 , and filling a varying-section channel of length L and halfaperture h(x) = h 0 − h 1 cos (2πx/L) and whose walls, flat along the z direction, have either a constant surface charge σ or a constant electrostatic potential ζ. The geometric impact of the channel corrugation on the electrokinetics of the liquid can be quantified in terms of the entropic barrier ∆S = ln h0+h1 h0−h1 [21]. In this highly confined geometry we consider that the channel aperture varies smoothly, ∂ x h(x) ≪ 1.…”

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Entropic Electrokinetics: Recirculation, Particle Separation, and Negative Mobility

2014

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We show that when particles are suspended in an electrolyte confined between corrugated charged surfaces, electrokinetic flows lead to a new set of phenomena such as particle separation, mixing for low-Reynolds micro-and nano-metric devices and negative mobility. Our analysis shows that such phenomena arise, for incompressible fluids, due to the interplay between the electrostatic double layer and the corrugated geometrical confinement and that they are magnified when the width of the channel is comparable to the Debye length. Our characterization allows us to understand the physical origin of such phenomena therefore shading light on their possible relevance in a wide variety of situations, ranging from nano-and micro-fluidic devices to biological systems.PACS numbers: 82.39. Wj,47.56.+r,47.61.Fg The recent development of nano-and micro-fluidic devices [1] as well as cellular regulation mechanisms and cellular signaling [2] rely on the transport of ions across channels or pores whose sections range from the nanometric to the micrometric scale [3][4][5]. The transport across such conduits has been characterized, even for varying-section channels [6][7][8][9][10][11], assuming that the channel width, h(x), is large compared to the Debye length, κ −1 , over which the electrolyte charge distributes in the neighborhood of the charged channel wall (κh(x) ≫ 1), or in the absence of electrolytes [12]. Nowadays, the continuous process of device miniaturization and the widening of the range of achievable salt concentrations require an understanding of the behavior of such systems when the relevant length scales compete with each other [13]. Such regimes are already exploitable in different microand nano-fluidic experiments [3,4] and can be relevant in a variety of biological systems [14,15].In this Letter we will show that, precisely in this regime, i.e. when the Debye length and the channel aperture are comparable in size, κh(x) ∼ 1, an electrolyte embedded in a corrugated channel develops new transport regimes that can be exploited to separate suspended particles, control electric and mass currents and eventually induce negative mobility. When κh(x) ∼ 1, the electrolyte response to external forcing, such as electrostatic fields, is very sensitive to the channel shape and it develops a recirculating region in which the electrolyte flows on the opposite direction as compared to the average volume flow, as shown in Fig. 1.A. Such a phenomenon, typical for incompressible fluids, is due to the interplay between the electrostatic double layer and the varying geometrical confinement and its magnitude is significantly amplified when κh(x) ∼ 1. We coin this regime entropic electrokinetics since the phenomena we identify can only arise due to the spatially varying constriction induced by the geometrical confinement. This variation affects the local spatial distribution of ions, essentially controlled by the interplay between the wall charge and the ion entropy. We will show that the entropic variations in the charge density i...

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Confined Brownian ratchets

Cited by 60 publications

References 30 publications

Intracellular transport driven by cytoskeletal motors: General mechanisms and defects

Intracellular transport driven by cytoskeletal motors: General mechanisms and defects

Non-monotonous polymer translocation time across corrugated channels: Comparison between Fick-Jacobs approximation and numerical simulations

Entropic Electrokinetics: Recirculation, Particle Separation, and Negative Mobility

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