arXiv subjects

R. Voituriez

Publications and source records attributed to R. Voituriez.

At least 55 records · Page 3Linked to original sources

arXiv2009

Robustness of optimal intermittent search strategies in dimension 1, 2 and 3

Search problems at various scales involve a searcher, be it a molecule before reaction or a foraging animal, which performs an intermittent motion. Here we analyze a generic model based on such type of intermittent motion, in which the searcher alternates phases of slow motion allowing detection, and phases of fast motion without detection. We present full and systematic results for different modeling hypotheses of the detection mechanism in space dimension 1, 2 and 3. Our study completes and extends the results of our recent letter [Loverdo {\it et al.} Nature Physics {\bf 4}, 134 (2008)] and gives the necessary calculation details. In addition, a new modeling of the detection phase is presented. We show that the mean target detection time can be minimized as a function of the mean duration of each phase in dimension 1, 2 and 3. Importantly, this optimal strategy does not depend on the details of the modeling of the slow detection phase, which shows the robustness of our results. We believe that this systematic analysis can be used as a basis to study quantitatively various real search problems involving intermittent behaviors.

cond-mat.stat-mech↗

arXiv2009

Global mean first-passage times of random walks on complex networks

We present a general framework, applicable to a broad class of random walks on complex networks, which provides a rigorous lower bound for the mean first-passage time of a random walker to a target site averaged over its starting position, the so-called global mean first-passage time (GMFPT). This bound is simply expressed in terms of the equilibrium distribution at the target, and implies a minimal scaling of the GMFPT with the network size. We show that this minimal scaling, which can be arbitrarily slow for a proper choice of highly connected target, is realized under the simple condition that the random walk is transient at the target site, and independently of the small-world, scale free or fractal properties of the network. Last, we put forward that the GMFPT to a specific target is not a representative property of the network, since the target averaged GMFPT satisfies much more restrictive bounds, which forbid any sublinear scaling with the network size.

cond-mat.stat-mech↗

arXiv2009

Pushing off the walls: a mechanism of cell motility in confinement

We propose a novel mechanism of cell motility, which relies on the coupling of actin polymerization at the cell membrane to geometric confinement. We consider a polymerizing viscoelastic cytoskeletal gel confined in a narrow channel, and show analytically that spontaneous motion occurs. Interestingly, this does not require specific adhesion with the channel walls, and yields velocities potentially larger than the polymerization velocity. The contractile activity of myosin motors is not necessary to trigger motility in this mechanism, but is shown quantitatively to increase the velocity. Our model qualitatively accounts for recent experiments which show that cells without specific adhesion proteins are motile only in confined environments while they are unable to move on a flat surface, and could help in understanding the mechanisms of cell migration in more complex confined geometries such as living tissues.

cond-mat.soft↗

arXiv2009

Searching fast for a target on a DNA without falling to traps

Genomic expression depends critically both on the ability of regulatory proteins to locate specific target sites on a DNA within seconds and on the formation of long lived (many minutes) complexes between these proteins and the DNA. Equilibrium experiments show that indeed regulatory proteins bind tightly to their target site. However, they also find strong binding to other non-specific sites which act as traps that can dramatically increase the time needed to locate the target. This gives rise to a conflict between the speed and stability requirements. Here we suggest a simple mechanism which can resolve this long-standing paradox by allowing the target sites to be located by proteins within short time scales even in the presence of traps. Our theoretical analysis shows that the mechanism is robust in the presence of generic disorder in the DNA sequence and does not require a specially designed target site.

cond-mat.soft↗

arXiv2008

Generic phase diagram of active polar films

We study theoretically the phase diagram of compressible active polar gels such as the actin network of eukaryotic cells. Using generalized hydrodynamics equations, we perform a linear stability analysis of the uniform states in the case of an infinite bidimensional active gel to obtain the dynamic phase diagram of active polar films. We predict in particular modulated flowing phases, and a macroscopic phase separation at high activity. This qualitatively accounts for experimental observations of various active systems, such as acto-myosin gels, microtubules and kinesins in vitro solutions, or swimming bacterial colonies.

cond-mat.soft↗

arXiv2008

Probing microscopic origins of confined subdiffusion by first-passage observables

Subdiffusive motion of tracer particles in complex crowded environments, such as biological cells, has been shown to be widepsread. This deviation from brownian motion is usually characterized by a sublinear time dependence of the mean square displacement (MSD). However, subdiffusive behavior can stem from different microscopic scenarios, which can not be identified solely by the MSD data. In this paper we present a theoretical framework which permits to calculate analytically first-passage observables (mean first-passage times, splitting probabilities and occupation times distributions) in disordered media in any dimensions. This analysis is applied to two representative microscopic models of subdiffusion: continuous-time random walks with heavy tailed waiting times, and diffusion on fractals. Our results show that first-passage observables provide tools to unambiguously discriminate between the two possible microscopic scenarios of subdiffusion. Moreover we suggest experiments based on first-passage observables which could help in determining the origin of subdiffusion in complex media such as living cells, and discuss the implications of anomalous transport to reaction kinetics in cells.

cond-mat.stat-mech↗

arXiv2008

Enhanced reaction kinetics in biological cells

The cell cytoskeleton is a striking example of "active" medium driven out-of-equilibrium by ATP hydrolysis. Such activity has been shown recently to have a spectacular impact on the mechanical and rheological properties of the cellular medium, as well as on its transport properties : a generic tracer particle freely diffuses as in a standard equilibrium medium, but also intermittently binds with random interaction times to motor proteins, which perform active ballistic excursions along cytoskeletal filaments. Here, we propose for the first time an analytical model of transport limited reactions in active media, and show quantitatively how active transport can enhance reactivity for large enough tracers like vesicles. We derive analytically the average interaction time with motor proteins which optimizes the reaction rate, and reveal remarkable universal features of the optimal configuration. We discuss why active transport may be beneficial in various biological examples: cell cytoskeleton, membranes and lamellipodia, and tubular structures like axons.

cond-mat.stat-mech↗

arXiv2007

The narrow escape problem revisited

The time needed for a particle to exit a confining domain through a small window, called the narrow escape time (NET), is a limiting factor of various processes, such as some biochemical reactions in cells. Obtaining an estimate of the mean NET for a given geometric environment is therefore a requisite step to quantify the reaction rate constant of such processes, which has raised a growing interest in the last few years. In this Letter, we determine explicitly the scaling dependence of the mean NET on both the volume of the confining domain and the starting point to aperture distance. We show that this analytical approach is applicable to a very wide range of stochastic processes, including anomalous diffusion or diffusion in the presence of an external force field, which cover situations of biological relevance.

cond-mat.stat-mech↗

arXiv2007

Comment on "Localization Transition of Biased Random Walks on Random Networks"

Sood and Grassberger studied in [Phys. Rev. Lett. 99, 098701 (2007)] random walks on random graphs that are biased towards a fixed target point. They put forward a critical bias strength b_c such that a random walker on an infinite graph eventually reaches the target with probability 1 when b>b_c, while a finite fraction of walks drift off to infinity for b<b_c. They rely on rigorous results obtained for biased walks on Galton-Watson (GW) trees to calculate b_c, and give arguments indicating that this result should also hold for random graphs such as Erdos-Renyi (ER) graphs and Molloy-Reed (MR) graphs. To validate their prediction, they show by numerical simulations that the mean return time (MRT) on a finite ER graph, as a function of the graph size N, exhibits a transition around the expected b_c. Here we show that the MRT on a GW tree can actually be computed analytically. This allows us (i) to show analytically that indeed the MRT displays a transition at b_c, (ii) to elucidate the N dependence of the MRT, which contradicts the \propto N scaling expected in [Phys. Rev. Lett. 99, 098701 (2007)] for b<b_c.

cond-mat.stat-mech↗

arXiv2007

First-passage times in complex scale-invariant media

How long does it take a random walker to reach a given target point? This quantity, known as a first passage time (FPT), has led to a growing number of theoretical investigations over the last decade1. The importance of FPTs originates from the crucial role played by first encounter properties in various real situations, including transport in disordered media, neuron firing dynamics, spreading of diseases or target search processes. Most methods to determine the FPT properties in confining domains have been limited to effective 1D geometries, or for space dimensions larger than one only to homogeneous media1. Here we propose a general theory which allows one to accurately evaluate the mean FPT (MFPT) in complex media. Remarkably, this analytical approach provides a universal scaling dependence of the MFPT on both the volume of the confining domain and the source-target distance. This analysis is applicable to a broad range of stochastic processes characterized by length scale invariant properties. Our theoretical predictions are confirmed by numerical simulations for several emblematic models of disordered media, fractals, anomalous diffusion and scale free networks.

cond-mat.stat-mech↗

arXiv2006

Random patterns generated by random permutations of natural numbers

We survey recent results on some one- and two-dimensional patterns generated by random permutations of natural numbers. In the first part, we discuss properties of random walks, evolving on a one-dimensional regular lattice in discrete time $n$, whose moves to the right or to the left are induced by the rise-and-descent sequence associated with a given random permutation. We determine exactly the probability of finding the trajectory of such a permutation-generated random walk at site $X$ at time $n$, obtain the probability measure of different excursions and define the asymptotic distribution of the number of "U-turns" of the trajectories - permutation "peaks" and "through". In the second part, we focus on some statistical properties of surfaces obtained by randomly placing natural numbers $1,2,3, >...,L$ on sites of a 1d or 2d square lattices containing $L$ sites. We calculate the distribution function of the number of local "peaks" - sites the number at which is larger than the numbers appearing at nearest-neighboring sites - and discuss some surprising collective behavior emerging in this model.

cond-mat.stat-mech↗

arXiv2006

Bidimensional intermittent search processes: an alternative to Levy flights strategies

Levy flights are known to be optimal search strategies in the particular case of revisitable targets. In the relevant situation of non revisitable targets, we propose an alternative model of bidimensional search processes, which explicitly relies on the widely observed intermittent behavior of foraging animals. We show analytically that intermittent strategies can minimize the search time, and therefore do constitute real optimal strategies. We study two representative modes of target detection, and determine which features of the search time are robust and do not depend on the specific characteristics of detection mechanisms. In particular, both modes lead to a global minimum of the search time as a function of the typical times spent in each state, for the same optimal duration of the ballistic phase. This last quantity could be a universal feature of bidimensional intermittent search strategies.

cond-mat.stat-mech↗

arXiv2005

Averaged residence times of stochastic motions in bounded domains

Two years ago, Blanco and Fournier (Blanco S. and Fournier R., Europhys. Lett. 2003) calculated the mean first exit time of a domain of a particle undergoing a randomly reoriented ballistic motion which starts from the boundary. They showed that it is simply related to the ratio of the volume's domain over its surface. This work was extended by Mazzolo (Mazzolo A., Europhys. Lett. 2004) who studied the case of trajectories which start inside the volume. In this letter, we propose an alternative formulation of the problem which allows us to calculate not only the mean exit time, but also the mean residence time inside a sub-domain. The cases of any combinations of reflecting and absorbing boundary conditions are considered. Lastly, we generalize our results for a wide class of stochastic motions.

cond-mat.stat-mech↗

arXiv2005

Optimal search strategies for hidden targets

What is the fastest way of finding a randomly hidden target? This question of general relevance is of vital importance for foraging animals. Experimental observations reveal that the search behaviour of foragers is generally intermittent: active search phases randomly alternate with phases of fast ballistic motion. In this letter, we study the efficiency of this type of two states search strategies, by calculating analytically the mean first passage time at the target. We model the perception mecanism involved in the active search phase by a diffusive process. In this framework, we show that the search strategy is optimal when the average duration of "motion phases" varies like the power either 3/5 or 2/3 of the average duration of "search phases", depending on the regime. This scaling accounts for experimental data over a wide range of species, which suggests that the kinetics of search trajectories is a determining factor optimized by foragers and that the perception activity is adequately described by a diffusion process.

cond-mat.stat-mech↗

arXiv2005

Spontaneous flow transition in active polar gels

We study theoretically the effects of confinement on active polar gels such as the actin network of eukaryotic cells. Using generalized hydrodynamics equations derived for active gels, we predict, in the case of quasi one-dimensional geometry, a spontaneous flow transition from a homogeneously polarized immobile state for small thicknesses, to a perturbed flowing state for larger thicknesses. The transition is not driven by an external field but by the activity of the system. We suggest several possible experimental realizations.

q-bio.SC↗

arXiv2005

Corrections to the Law of Mass Action and Properties of the Asymptotic $t = \infty$ State for Reversible Diffusion-Limited Reactions

On example of diffusion-limited reversible $A+A \rightleftharpoons B$ reactions we re-examine two fundamental concepts of classical chemical kinetics - the notion of "Chemical Equilibrium" and the "Law of Mass Action". We consider a general model with distance-dependent reaction rates, such that any pair of $A$ particles, performing standard random walks on sites of a $d$-dimensional lattice and being at a distance $μ$ apart of each other at time moment $t$, may associate forming a $B$ particle at the rate $k_+(μ)$. In turn, any randomly moving $B$ particle may spontaneously dissociate at the rate $k_-(λ)$ into a geminate pair of $A$s "born" at a distance $λ$ apart of each other. Within a formally exact approach based on Gardiner's Poisson representation method we show that the asymptotic $t = \infty$ state attained by such diffusion-limited reactions is generally \textit{not a true thermodynamic equilibrium}, but rather a non-equilibrium steady-state, and that the Law of Mass Action is invalid. The classical concepts hold \text{only} in case when the ratio $k_+(μ)/k_-(μ)$ does not depend on $μ$ for any $μ$.

cond-mat.stat-mech↗

arXiv2005

Kinetics of target site localization of a protein on DNA: a stochastic approach

It is widely recognized that the cleaving rate of a restriction enzyme on target DNA sequences is several orders of magnitude faster than the maximal one calculated from the diffusion--limited theory. It was therefore commonly assumed that the target site interaction of a restriction enzyme with DNA has to occur via two steps: one--dimensional diffusion along a DNA segment, and long--range jumps coming from association/dissociation events. We propose here a stochastic model for this reaction which comprises a series of 1D diffusions of a restriction enzyme on non-specific DNA sequences interrupted by 3D excursions in the solution until the target sequence is reached. This model provides an optimal finding strategy which explains the fast association rate. Modeling the excursions by uncorrelated random jumps, we recover the expression of the mean time required for target site association to occur given by Berg & al. \cite{berg81}, and we explicitly give several physical quantities describing the stochastic pathway of the enzyme. For competitive target sites we calculate two quantities: processivity and preference. By comparing these theoretical expressions to recent experimental data obtained for \textit{Eco}RV--DNA interaction, we quantify: i) the mean residence time per binding event of \textit{Eco}RV on DNA for a representative 1D diffusion coefficient, ii) the average lengths of DNA scanned during the 1D diffusion (during one binding event and during the overall process), iii) the mean time and the mean number of visits needed to go from one target site to the other. Further, we evaluate the dynamics of DNA cleavage with regard to the probability for the restriction enzyme to perform another 1D diffusion on the same DNA substrate following a 3D excursion.

q-bio.SC↗

arXiv2004

Random walk generated by random permutations of {1,2,3, ..., n+1}

We study properties of a non-Markovian random walk $X^{(n)}_l$, $l =0,1,2, >...,n$, evolving in discrete time $l$ on a one-dimensional lattice of integers, whose moves to the right or to the left are prescribed by the \text{rise-and-descent} sequences characterizing random permutations $π$ of $[n+1] = \{1,2,3, ...,n+1\}$. We determine exactly the probability of finding the end-point $X_n = X^{(n)}_n$ of the trajectory of such a permutation-generated random walk (PGRW) at site $X$, and show that in the limit $n \to \infty$ it converges to a normal distribution with a smaller, compared to the conventional Pólya random walk, diffusion coefficient. We formulate, as well, an auxiliary stochastic process whose distribution is identic to the distribution of the intermediate points $X^{(n)}_l$, $l < n$, which enables us to obtain the probability measure of different excursions and to define the asymptotic distribution of the number of "turns" of the PGRW trajectories.

cond-mat.stat-mech↗