arXiv subjects

R. Voituriez

Publications and source records attributed to R. Voituriez.

At least 37 records · Page 2Linked to original sources

arXiv2013

Fluctuations and correlations of a driven tracer in a hard-core lattice gas

We consider a driven tracer particle (TP) in a bath of hard-core particles undergoing continuous exchanges with a reservoir. We develop an analytical framework which allows us to go beyond the standard force-velocity relation used for this minimal model of active microrheology and quantitatively analyze, for any density of the bath particles, the fluctuations of the TP position and their correlations with the occupation number of the bath particles. We obtain an exact Einstein-type relation which links these fluctuations in the absence of a driving force and the bath particles density profiles in the linear driving regime. For the one-dimensional case we also provide an approximate but very accurate explicit expression for the variance of the TP position and show that it can be a non-monotoneous function of the bath particles density: counter-intuitively, an increase of the density may increase the dispersion of the TP position. We show that this non trivial behavior, which could in principle be observed in active microrheology experiments, is induced by subtle cross-correlations quantified by our approach.

cond-mat.stat-mech↗

arXiv2013

Active transport in dense diffusive single-file systems

We study a minimal model of active transport in crowded single-file environments which generalises the emblematic model of single file diffusion to the case when the tracer particle (TP) performs either an autonomous directed motion or is biased by an external force, while all other particles of the environment (bath) perform unbiased diffusions. We derive explicit expressions, valid in the limit of high density of bath particles, of the full distribution $P_n(X)$ of the TP position and of all its cumulants, for arbitrary values of the bias $f$ and for any time $n$. Our analysis reveals striking features, such as the anomalous scaling $\propto\sqrt{n}$ of all cumulants, the equality of cumulants of the same parity characteristic of a Skellam distribution and a convergence to a Gaussian distribution in spite of asymmetric density profiles of bath particles. Altogether, our results provide the full statistics of the TP position, and set the basis for a refined analysis of real trajectories of active particles in crowded single-file environments.

cond-mat.stat-mech↗

arXiv2013

Active Gel Model of Amoeboid Cell Motility

We develop a model of amoeboid cell motility based on active gel theory. Modeling the motile apparatus of a eukaryotic cell as a confined layer of finite length of poroelastic active gel permeated by a solvent, we first show that, due to active stress and gel turnover, an initially static and homogeneous layer can undergo a contractile-type instability to a polarized moving state in which the rear is enriched in gel polymer. This agrees qualitatively with motile cells containing an actomyosin-rich uropod at their rear. We find that the gel layer settles into a steadily moving, inhomogeneous state at long times, sustained by a balance between contractility and filament turnover. In addition, our model predicts an optimal value of the gel-susbstrate adhesion leading to maximum layer speed, in agreement with cell motility assays. The model may be relevant to motility of cells translocating in complex, confining environments that can be mimicked experimentally by cell migration through microchannels.

physics.bio-ph↗

arXiv2012

Reactive conformations and non-Markovian cyclization kinetics of a Rouse polymer

We investigate theoretically the physics of diffusion-limited intramolecular polymer reactions. The present work completes and goes beyond a previous study [Nat. Chem. 4, 268 (2012)] that showed that the distribution of the polymer conformations at the very instant of reaction plays a key role in the cyclization kinetics, and takes explicitly into account the non-Markovian nature of the reactant motion. Here, we present in detail this non-Markovian theory, and compare it explicitly with existing Markovian theories and with numerical stochastic simulations. A large focus is made on the description of the non-equilibrium reactive conformations, with both numerical and analytical tools. We show that the reactive conformations are elongated and are characterized by a spectrum with a slowly decreasing tail, implying that the monomers that neighbor the reactive monomers are significantly shifted at the instant of reaction. We complete the study by deriving explicit formulas for the reaction rates in the Markovian Wilemski-Fixman theory when the reactants are located in arbitrary positions in the chain. We also give a simple scaling argument to understand the existence of two regimes in the reaction time, that come from two possible behaviors of monomer motion which can be either diffusive or subdiffusive.

cond-mat.stat-mech↗

arXiv2012

Exact mean exit time for surface-mediated diffusion

We present an exact expression for the mean exit time through the cap of a confining sphere for particles alternating phases of surface and of bulk diffusion. The present approach is based on an integral equation which can be solved analytically. In contrast to the statement of Berezhkovskii and Barzykin [J. Chem. Phys. 136, 54115 (2012)], we show that the mean exit time can be optimized with respect to the desorption rate, under analytically determined criteria.

cond-mat.stat-mech↗

arXiv2012

Reactive conformations and non-Markovian reaction kinetics of a Rouse polymer searching for a target in confinement

We investigate theoretically a diffusion-limited reaction between a reactant attached to a Rouse polymer and an external fixed reactive site in confinement. The present work completes and goes beyond a previous study [T. Guérin, O. Bénichou and R. Voituriez, Nat. Chem., 4, 268 (2012)] that showed that the distribution of the polymer conformations at the very instant of reaction plays a key role in the reaction kinetics, and that its determination enables the inclusion of non-Markovian effects in the theory. Here, we describe in detail this non-Markovian theory and we compare it with numerical stochastic simulations and with a Markovian approach, in which the reactive conformations are approximated by equilibrium ones. We establish the following new results. Our analysis reveals a strongly non-Markovian regime in 1D, where the Markovian and non-Markovian dependance of the relation time on the initial distance are different. In this regime, the reactive conformations are so different from equilibrium conformations that the Markovian expressions of the reaction time can be overestimated by several orders of magnitudes for long chains. We also show how to derive qualitative scaling laws for the reaction time in a systematic way that takes into account the different behaviors of monomer motion at all time and length scales. Finally, we also give an analytical description of the average elongated shape of the polymer at the instant of the reaction and we show that its spectrum behaves a a slow power-law for large wave numbers.

cond-mat.stat-mech↗

arXiv2012

Kinetics of active surface-mediated diffusion in spherically symmetric domains

We present an exact calculation of the mean first-passage time to a target on the surface of a 2D or 3D spherical domain, for a molecule alternating phases of surface diffusion on the domain boundary and phases of bulk diffusion. We generalize the results of [J. Stat. Phys. {\bf 142}, 657 (2011)] and consider a biased diffusion in a general annulus with an arbitrary number of regularly spaced targets on a partially reflecting surface. The presented approach is based on an integral equation which can be solved analytically. Numerically validated approximation schemes, which provide more tractable expressions of the mean first-passage time are also proposed. In the framework of this minimal model of surface-mediated reactions, we show analytically that the mean reaction time can be minimized as a function of the desorption rate from the surface.

cond-mat.stat-mech↗

arXiv2012

Non-Gaussianity and Dynamical Trapping in Locally Activated Random Walks

We propose a minimal model of \emph{locally-activated diffusion}, in which the diffusion coefficient of a one-dimensional Brownian particle is modified in a prescribed way --- either increased or decreased --- upon each crossing of the origin. Such a local mobility decrease arises in the formation of atherosclerotic plaques due to diffusing macrophage cells accumulating lipid particles. We show that spatially localized mobility perturbations have remarkable consequences on diffusion at all scales, such as the emergence of a non-Gaussian multi-peaked probability distribution and a dynamical transition to an absorbing static state. In the context of atherosclerosis, this dynamical transition can be viewed as a minimal mechanism that causes macrophages to aggregate in lipid-enriched regions and thereby to the formation of atherosclerotic plaques.

cond-mat.stat-mech↗

arXiv2012

Optimizing persistent random searches

We consider a minimal model of persistent random searcher with short range memory. We calculate exactly for such searcher the mean first-passage time to a target in a bounded domain and find that it admits a non trivial minimum as function of the persistence length. This reveals an optimal search strategy which differs markedly from the simple ballistic motion obtained in the case of Poisson distributed targets. Our results show that the distribution of targets plays a crucial role in the random search problem. In particular, in the biologically relevant cases of either a single target or regular patterns of targets, we find that, in strong contrast with repeated statements in the literature, persistent random walks with exponential distribution of excursion lengths can minimize the search time, and in that sense perform better than any Levy walk.

cond-mat.stat-mech↗

arXiv2012

Exact calculations of first-passage quantities on recursive networks

We present general methods to exactly calculate mean-first passage quantities on self-similar networks defined recursively. In particular, we calculate the mean first-passage time and the splitting probabilities associated to a source and one or several targets; averaged quantities over a given set of sources (e.g., same-connectivity nodes) are also derived. The exact estimate of such quantities highlights the dependency of first-passage processes with respect to the source-target distance, which has recently revealed to be a key parameter to characterize transport in complex media. We explicitly perform calculations for different classes of recursive networks (finitely ramified fractals, scale-free (trans)fractals, non-fractals, mixtures between fractals and non-fractals, non-decimable hierarchical graphs) of arbitrary size. Our approach unifies and significantly extends the available results in the field.

cond-mat.stat-mech↗

arXiv2011

Classes of fast and specific search mechanisms for proteins on DNA

Problems of search and recognition appear over different scales in biological systems. In this review we focus on the challenges posed by interactions between proteins, in particular transcription factors, and DNA and possible mechanisms which allow for a fast and selective target location. Initially we argue that DNA-binding proteins can be classified, broadly, into three distinct classes which we illustrate using experimental data. Each class calls for a different search process and we discuss the possible application of different search mechanisms proposed over the years to each class. The main thrust of this review is a new mechanism which is based on barrier discrimination. We introduce the model and analyze in detail its consequences. It is shown that this mechanism applies to all classes of transcription factors and can lead to a fast and specific search. Moreover, it is shown that the mechanism has interesting transient features which allow for stability at the target despite rapid binding and unbinding of the transcription factor from the target.

q-bio.BM↗

arXiv2011

Intermittent search strategies

This review examines intermittent target search strategies, which combine phases of slow motion, allowing the searcher to detect the target, and phases of fast motion during which targets cannot be detected. We first show that intermittent search strategies are actually widely observed at various scales. At the macroscopic scale, this is for example the case of animals looking for food ; at the microscopic scale, intermittent transport patterns are involved in reaction pathway of DNA binding proteins as well as in intracellular transport. Second, we introduce generic stochastic models, which show that intermittent strategies are efficient strategies, which enable to minimize the search time. This suggests that the intrinsic efficiency of intermittent search strategies could justify their frequent observation in nature. Last, beyond these modeling aspects, we propose that intermittent strategies could be used also in a broader context to design and accelerate search processes.

cond-mat.stat-mech↗

arXiv2011

Mean first-passage time of surface-mediated diffusion in spherical domains

We present an exact calculation of the mean first-passage time to a target on the surface of a 2D or 3D spherical domain, for a molecule alternating phases of surface diffusion on the domain boundary and phases of bulk diffusion. The presented approach is based on an integral equation which can be solved analytically. Numerically validated approximation schemes, which provide more tractable expressions of the mean first-passage time are also proposed. In the framework of this minimal model of surface-mediated reactions, we show analytically that the mean reaction time can be minimized as a function of the desorption rate from the surface.

cond-mat.stat-mech↗

arXiv2011

Facilitated diffusion of proteins on chromatin

We present a theoretical model of facilitated diffusion of proteins in the cell nucleus. This model, which takes into account the successive binding/unbinding events of proteins to DNA, relies on a fractal description of the chromatin which has been recently evidenced experimentally. Facilitated diffusion is shown quantitatively to be favorable for a fast localization of a target locus by a transcription factor, and even to enable the minimization of the search time by tuning the affinity of the transcription factor with DNA. This study shows the robustness of the facilitated diffusion mechanism, invoked so far only for linear conformations of DNA.

cond-mat.stat-mech↗

arXiv2010

Optimal reaction time for surface-mediated diffusion

We present an exact calculation of the mean first-passage time to a small target on the surface of a 2D or 3D spherical domain, for a molecule performing surface-mediated diffusion. This minimal model of interfacial reactions, which explicitly takes into account the combination of surface and bulk diffusion, shows the importance of correlations induced by the coupling of the switching dynamics to the geometry of the confinement, ignored so far. Interestingly, our results show that, in the context of interfacial systems in confinement, the reaction time can be minimized as a function of the desorption rate from the surface, which puts forward a general mechanism of enhancement and regulation of chemical reactivity.

cond-mat.stat-mech↗

arXiv2010

Spontaneous contractility--mediated cortical flow generates cell migration in 3-dimensional environments

We present a generic model of cell motility generated by acto-myosin contraction of the cell cortex. We identify analytically dynamical instabilities of the cortex and show that they trigger spontaneous cortical flows which in turn can induce cell migration in 3-dimensional (3D) environments as well as bleb formation. This contractility--based mechanism, widely independent of actin treadmilling, appears as an alternative to the classical picture of lamellipodial motility on flat substrates. Theoretical predictions are compared to experimental data of tumor cells migrating in 3D matrigel and suggest that this mechanism could be a general mode of cell migration in 3D environments.

q-bio.CB↗

arXiv2010

Optimization of the residence time of a Brownian particle in a spherical subdomain

In this communication, we show that the residence time of a Brownian particle, defined as the cumulative time spent in a given region of space, can be optimized as a function of the diffusion coefficient. We discuss the relevance of this effect to several schematic experimental situations, classified in the nature -- random or deterministic -- both of the observation time and of the starting position of the Brownian particle.

cond-mat.stat-mech↗

arXiv2010

Geometry-controlled kinetics

It has long been appreciated that transport properties can control reaction kinetics. This effect can be characterized by the time it takes a diffusing molecule to reach a target -- the first-passage time (FPT). Although essential to quantify the kinetics of reactions on all time scales, determining the FPT distribution was deemed so far intractable. Here, we calculate analytically this FPT distribution and show that transport processes as various as regular diffusion, anomalous diffusion, diffusion in disordered media and in fractals fall into the same universality classes. Beyond this theoretical aspect, this result changes the views on standard reaction kinetics. More precisely, we argue that geometry can become a key parameter so far ignored in this context, and introduce the concept of "geometry-controlled kinetics". These findings could help understand the crucial role of spatial organization of genes in transcription kinetics, and more generally the impact of geometry on diffusion-limited reactions.

cond-mat.stat-mech↗