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Raphaël Voituriez

Publications and source records attributed to Raphaël Voituriez.

33 records · Page 2Linked to original sources
arXiv2019

Diffusion through nanopores in connected lipid bilayer networks

A biomimetic model of cell-cell communication was developed to probe the passive molecular transport across ion channels inserted in synthetic lipid bilayers formed between contacting droplets arranged in a linear array. Diffusion of a fluorescent probe across the array was measured for different pore concentrations. The diffusion characteristic time scale is found to vary non-linearly with the pore concentration. Our measurements are successfully modeled by a continuous time random walk description, whose waiting time is the first exit time from a droplet through a cluster of pores. The size of the cluster of pores is found to increase with their concentration. Our results provide a direct link between the mesoscopic permeation properties and the microscopic characteristics of the pores such as their number, size and spatial arrangement.

physics.bio-ph↗
arXiv2018

Dynamics of Run-and-Tumble Particles in Dense Single-File Systems

We study a minimal model of self-propelled particle in a crowded single-file environment. We extend classical models of exclusion processes (previously analyzed for diffusive and driven tracer particles) to the case where the tracer particle is a run-and-tumble particle (RTP), while all bath particles perform symmetric random walks. In the limit of high density of bath particles, we derive exact expressions for the full distribution $\mathcal{P}_n(X)$ of the RTP position $X$ and all its cumulants, valid for arbitrary values of the tumbling probability $α$ and time $n$. Our results highlight striking effects of crowding on the dynamics: even cumulants of the RTP position are increasing functions of $α$ at intermediate timescales, and display a subdiffusive anomalous scaling $\propto \sqrt{n}$ independent of $α$ in the limit of long times $n\to \infty$. These analytical results set the ground for a quantitative analysis of experimental trajectories of real biological or artificial microswimmers in extreme confinement.

cond-mat.stat-mech↗
arXiv2018

Optimized Diffusion of Run-and-Tumble Particles in Crowded Environments

We study the transport of self-propelled particles in dynamic complex environments. To obtain exact results, we introduce a model of run-and-tumble particles (RTPs) moving in discrete time on a $d$-dimensional cubic lattice in the presence of diffusing hard core obstacles. We derive an explicit expression for the diffusivity of the RTP, which is exact in the limit of low density of fixed obstacles. To do so, we introduce a generalization of Kac's theorem on the mean return times of Markov processes, which we expect to be relevant for a large class of lattice gas problems. Our results show the diffusivity of RTPs to be nonmonotonic in the tumbling probability for low enough obstacle mobility. These results prove the potential for optimization of the transport of RTPs in crowded and disordered environments with applications to motile artificial and biological systems.

cond-mat.stat-mech↗
arXiv2018

Nonequilibrium fluctuations and enhanced diffusion of a driven particle in a dense environment

We study the diffusion of a tracer particle driven out-of-equilibrium by an external force and traveling in a dense environment of arbitrary density. The system evolves on a discrete lattice and its stochastic dynamics is described by a master equation. Relying on a decoupling approximation that goes beyond the naive mean-field treatment of the problem, we calculate the fluctuations of the position of the tracer around its mean value on a lattice of arbitrary dimension, and with different boundary conditions. We reveal intrinsically nonequilibrium effects, such as enhanced diffusivity of the tracer induced both by the crowding interactions and the external driving. We finally consider the high-density and low-density limits of the model and show that our approximation scheme becomes exact in these limits.

cond-mat.stat-mech↗
arXiv2017

Non-Markovian closure kinetics of flexible polymers with hydrodynamic interactions

This paper presents a theoretical analysis of the closure kinetics of a polymer with hydrodynamic interactions. This analysis, which takes into account the non-Markovian dynamics of the end-to-end vector and relies on the preaveraging of the mobility tensor (Zimm dynamics), is shown to reproduce very accurately the results of numerical simulations of the complete non linear dynamics. It is found that Markovian treatments, based on a Wilemski-Fixman approximation, significantly overestimate cyclization times (up to a factor 2), showing the importance of memory effects in the dynamics. In addition, this analysis provides scaling laws of the mean first cyclization time (MFCT) with the polymer size $N$ and capture radius $b$, which are identical in both Markovian and non-Markovian approaches. In particular, it is found that the scaling of the MFCT for large $N$ is given by $T\sim N^{3/2}\ln (N/b^2)$, which differs from the case of the Rouse dynamics where $T\sim N^{2}$. The extension to the case of the reaction kinetics of a monomer of a Zimm polymer with an external target in a confined volume is also presented.

cond-mat.stat-mech↗
arXiv2017

Mean first-passage time of an anisotropic diffusive searcher

We consider an anisotropic needle-like Brownian particle with nematic symmetry confined in a $2D$ domain. For this system, the coupling of translational and rotational diffusion makes the process ${\bf x} (t)$ of the positions of the particle non Markovian. Using scaling arguments, a Gaussian approximation and numerical methods, we determine the mean first passage time $\langle\mathbf{T}\rangle$ of the particle to a target of radius $a$ and show in particular that $\langle\mathbf{T}\rangle \sim a^{-1/2}$ for $a\to 0$, in contrast with the classical logarithmic divergence obtained in the case of an isotropic $2D$ Brownian particle.

cond-mat.stat-mech↗
arXiv2016

Active particles with soft and curved walls: Equation of state, ratchets, and instabilities

We study, from first principles, the pressure exerted by an active fluid of spherical particles on general boundaries in two dimensions. We show that, despite the non-uniform pressure along curved walls, an equation of state is recovered upon a proper spatial averaging. This holds even in the presence of pairwise interactions between particles or when asymmetric walls induce ratchet currents, which are accompanied by spontaneous shear stresses on the walls. For flexible obstacles, the pressure inhomogeneities lead to a modulational instability as well as to the spontaneous motion of short semi-flexible filaments. Finally, we relate the force exerted on objects immersed in active baths to the particle flux they generate around them.

cond-mat.stat-mech↗
arXiv2015

Contact Kinetics in Fractal Macromolecules

We consider the kinetics of first contact between two monomers of the same macromolecule. Relying on a fractal description of the macromolecule, we develop an analytical method to compute the Mean First Contact Time (MFCT) for various molecular sizes. In our theoretical description, the non-Markovian feature of monomer motion, arising from the interactions with the other monomers, is captured by accounting for the non-equilibrium conformations of the macromolecule at the very instant of first contact. This analysis reveals a simple scaling relation for the MFCT between two monomers, which involves only their equilibrium distance and the spectral dimension of the macromolecule, independently of its microscopic details. Our theoretical predictions are in excellent agreement with numerical stochastic simulations.

cond-mat.soft↗
arXiv2015

Distribution of the position of a driven tracer in a hardcore lattice gas

We study the position of a biased tracer particle (TP) in a bath of hardcore particles moving on a lattice of arbitrary dimension and in contact with a reservoir. Starting from the master equation satisfied by the joint probability of the TP position and the bath configuration and resorting to a mean-field-type approximation, we presented a computation of the fluctuations of the TP position in a previous publication [Phys. Rev. E \textbf{87}, 032164 (2013)]. Counterintuitively, on a one-dimensional lattice, the diffusion coefficient of the TP was shown to be a non-monotonic function of the density of bath particles, and reaches a maximum for a nonzero value of the density. Here, we: (i) give the details of this computation and offer a physical insight into the understanding of the non-monotonicity of the diffusion coefficient; (ii) extend the mean-field-type approximation to decouple higher-order correlation functions, and obtain the evolution equation satisfied by the cumulant generating function of the position of the TP, valid in any space dimension. In the particular case of a one-dimensional lattice, we solve this equation and obtain the probability distribution of the TP position. We show that the position rescaled by its fluctuations is asymptotically distributed accordingly to a Gaussian distribution in the long-time limit.

cond-mat.stat-mech↗
arXiv2014

Mean cover time of one-dimensional persistent random walks

The cover time is defined as the time needed for a random walker to visit every site of a confined domain. Here, we focus on persistent random walks, which provide a minimal model of random walks with short range memory. We derive the exact expression of the mean cover time of a one-dimensional lattice by such a persistent random walk, both for periodic and reflecting boundary conditions.

cond-mat.stat-mech↗
arXiv2014

Active polar fluid flow in finite droplets

We present a continuum level analytical model of a droplet of active contractile fluid consisting of filaments and motors. We calculate the steady state flows that result from a splayed polarisation of the filaments. We account for the interaction with an arbitrary external medium by imposing a viscous friction at the fixed droplet boundary. We then show that the droplet has non-zero force dipole and quadrupole moments, the latter of which is essential for self-propelled motion of the droplet at low Reynolds' number. Therefore, this calculation describes a simple mechanism for the motility of a droplet of active contractile fluid embedded in a 3D environment, which is relevant to cell migration in confinement (for example, embedded within a gel or tissue). Our analytical results predict how the system depends on various parameters such as the effective friction coefficient, the phenomenological activity parameter and the splay of the imposed polarisation.

q-bio.CB↗
arXiv2013

Geometry-induced superdiffusion in driven crowded systems

Recent Molecular Dynamics simulations of glass-forming liquids revealed superdiffusive fluctuations associated with the position of a tracer particle (TP) driven by an external force. Such anomalous response, whose mechanism remains elusive, has been observed up to now only in systems close to their glass transition, suggesting that this could be one of its hallmarks. Here, we show that the presence of superdiffusion is in actual fact much more general, provided that the system is crowded and geometrically confined. We present and solve analytically a minimal model consisting of a driven TP in a dense, crowded medium in which the motion of particles is mediated by the diffusion of packing defects, called vacancies. For such non glass-forming systems, our analysis predicts a long-lived superdiffusion which ultimately crosses over to giant diffusive behavior. We find that this trait is present in confined geometries, for example long capillaries and stripes, and emerges as a universal response of crowded environments to an external force. These findings are confirmed by numerical simulations of systems as varied as lattice-gases, dense liquids and granular fluids.

cond-mat.stat-mech↗
arXiv2012

Taylor Dispersion with Adsorption and Desorption

We use a stochastic approach to show how Taylor dispersion is affected by kinetic processes of adsorption and desorption onto surfaces. A general theory is developed, from which we derive explicitly the dispersion coefficients of canonical examples like Poiseuille flows in planar and cylindrical geometries, both in constant and sinusoidal velocity fields. These results open the way for the measurement of adsorption and desorption rate constants using stationary flows and molecular sorting using the stochastic resonance of the adsorption and desorption processes with the oscillatory velocity field.

cond-mat.stat-mech↗
arXiv2012

Non-Markovian polymer reaction kinetics

Describing the kinetics of polymer reactions, such as the formation of loops and hairpins in nucleic acids or polypeptides, is complicated by the structural dynamics of their chains. Although both intramolecular reactions, such as cyclization, and intermolecular reactions have been studied extensively, both experimentally and theoretically, there is to date no exact explicit analytical treatment of transport-limited polymer reaction kinetics, even in the case of the simplest (Rouse) model of monomers connected by linear springs. We introduce a new analytical approach to calculate the mean reaction time of polymer reactions that encompasses the non-Markovian dynamics of monomer motion. This requires that the conformational statistics of the polymer at the very instant of reaction be determined, which provides, as a by-product, new information on the reaction path. We show that the typical reactive conformation of the polymer is more extended than the equilibrium conformation, which leads to reaction times significantly shorter than predicted by the existing classical Markovian theory.

physics.chem-ph↗