SearcharxivSearch

arXiv subjects

M. Vergassola

Publications and source records attributed to M. Vergassola.

At least 19 recordsLinked to original sources

Inferring maps of forces inside cell membrane microdomains

Mapping of the forces on biomolecules in cell membranes has spurred the development of effective labels, e.g. organic fluorophores and nanoparticles, to track trajectories of single biomolecules. Standard methods use particular statistics, namely the mean square displacement, to analyze the underlying dynamics. Here, we introduce general inference methods to fully exploit information in the experimental trajectories, providing sharp estimates of the forces and the diffusion coefficients in membrane microdomains. Rapid and reliable convergence of the inference scheme is demonstrated on trajectories generated numerically. The method is then applied to infer forces and potentials acting on the receptor of the $ε$-toxin labeled by lanthanide-ion nanoparticles. Our scheme is applicable to any labeled biomolecule and results show show its general relevance for membrane compartmentation.

physics.bio-ph

Inference in particle tracking experiments by passing messages between images

Methods to extract information from the tracking of mobile objects/particles have broad interest in biological and physical sciences. Techniques based on simple criteria of proximity in time-consecutive snapshots are useful to identify the trajectories of the particles. However, they become problematic as the motility and/or the density of the particles increases due to uncertainties on the trajectories that particles followed during the images' acquisition time. Here, we report an efficient method for learning parameters of the dynamics of the particles from their positions in time-consecutive images. Our algorithm belongs to the class of message-passing algorithms, known in computer science, information theory and statistical physics as Belief Propagation (BP). The algorithm is distributed, thus allowing parallel implementation suitable for computations on multiple machines without significant inter-machine overhead. We test our method on the model example of particle tracking in turbulent flows, which is particularly challenging due to the strong transport that those flows produce. Our numerical experiments show that the BP algorithm compares in quality with exact Markov Chain Monte-Carlo algorithms, yet BP is far superior in speed. We also suggest and analyze a random-distance model that provides theoretical justification for BP accuracy. Methods developed here systematically formulate the problem of particle tracking and provide fast and reliable tools for its extensive range of applications.

physics.data-an

Nonlinear dynamics of the viscoelastic Kolmogorov flow

The weakly nonlinear regime of a viscoelastic Navier--Stokes fluid is investigated. For the purely hydrodynamic case, it is known that large-scale perturbations tend to the minima of a Ginzburg-Landau free-energy functional with a double-well (fourth-order) potential. The dynamics of the relaxation process is ruled by a one-dimensional Cahn--Hilliard equation that dictates the hyperbolic tangent profiles of kink-antikink structures and their mutual interactions. For the viscoelastic case, we found that the dynamics still admits a formulation in terms of a Ginzburg--Landau free-energy functional. For sufficiently small elasticities, the phenomenology is very similar to the purely hydrodynamic case: the free-energy functional is still a fourth-order potential and slightly perturbed kink-antikink structures hold. For sufficiently large elasticities, a critical point sets in: the fourth-order term changes sign and the next-order nonlinearity must be taken into account. Despite the double-well structure of the potential, the one-dimensional nature of the problem makes the dynamics sensitive to the details of the potential. We analysed the interactions among these generalized kink-antikink structures, demonstrating their role in a new, elastic instability. Finally, consequences for the problem of polymer drag reduction are presented.

nlin.CD

Shear effects on passive scalar spectra

The effects of a large-scale shear on the energy spectrum of a passively advected scalar field are investigated. The shear is superimposed on a turbulent isotropic flow, yielding an Obukhov-Corrsin $k^{-5/3}$ scalar spectrum at small scales. Shear effects appear at large scales, where a different, anisotropic behavior is observed. The scalar spectrum is shown to behave as $k^{-4/3}$ for a shear fixed in intensity and direction. For other types of shear characteristics, the slope is generally intermediate between the -5/3 Obukhov-Corrsin's and the -1 Batchelor's values. The physical mechanisms at the origin of this behaviour are illustrated in terms of the motion of Lagrangian particles. They provide an explanation to the scalar spectra shallow and dependent on the experimental conditions observed in shear flows at moderate Reynolds numbers.

nlin.CD

The decay of homogeneous anisotropic turbulence

We present the results of a numerical investigation of three-dimensional decaying turbulence with statistically homogeneous and anisotropic initial conditions. We show that at large times, in the inertial range of scales: (i) isotropic velocity fluctuations decay self-similarly at an algebraic rate which can be obtained by dimensional arguments; (ii) the ratio of anisotropic to isotropic fluctuations of a given intensity falls off in time as a power law, with an exponent approximately independent of the strength of the fluctuation; (iii) the decay of anisotropic fluctuations is not self-similar, their statistics becoming more and more intermittent as time elapses. We also investigate the early stages of the decay. The different short-time behavior observed in two experiments differing by the phase organization of their initial conditions gives a new hunch on the degree of universality of small-scale turbulence statistics, i.e. its independence of the conditions at large scales.

nlin.CD

Active vs passive scalar turbulence

Active and passive scalars transported by an incompressible two-dimensional conductive fluid are investigated. It is shown that a passive scalar displays a direct cascade towards the small scales while the active magnetic potential builds up large-scale structures in an inverse cascade process. Correlations between scalar input and particle trajectories are found to be responsible for those dramatic differences as well as for the behavior of dissipative anomalies.

nlin.CD

Intermittency in two-dimensional Ekman-Navier-Stokes turbulence

We study the statistics of the vorticity field in two-dimensional Navier-Stokes turbulence with a linear Ekman friction. We show that the small-scale vorticity fluctuations are intermittent, as conjectured by Nam et al. [Phys. Rev. Lett. vol.84 (2000) 5134]. The small-scale statistics of vorticity fluctuations coincides with the one of a passive scalar with finite lifetime transported by the velocity field itself.

nlin.CD

Particles and fields in fluid turbulence

The understanding of fluid turbulence has considerably progressed in recent years. The application of the methods of statistical mechanics to the description of the motion of fluid particles, i.e. to the Lagrangian dynamics, has led to a new quantitative theory of intermittency in turbulent transport. The first analytical description of anomalous scaling laws in turbulence has been obtained. The underlying physical mechanism reveals the role of statistical integrals of motion in non-equilibrium systems. For turbulent transport, the statistical conservation laws are hidden in the evolution of groups of fluid particles and arise from the competition between the expansion of a group and the change of its geometry. By breaking the scale-invariance symmetry, the statistically conserved quantities lead to the observed anomalous scaling of transported fields. Lagrangian methods also shed new light on some practical issues, such as mixing and turbulent magnetic dynamo.

cond-mat.stat-mech

Statistical conservation laws in turbulent transport

We address the statistical theory of fields that are transported by a turbulent velocity field, both in forced and in unforced (decaying) experiments. We propose that with very few provisos on the transporting velocity field, correlation functions of the transported field in the forced case are dominated by statistically preserved structures. In decaying experiments (without forcing the transported fields) we identify infinitely many statistical constants of the motion, which are obtained by projecting the decaying correlation functions on the statistically preserved functions. We exemplify these ideas and provide numerical evidence using a simple model of turbulent transport. This example is chosen for its lack of Lagrangian structure, to stress the generality of the ideas.

nlin.CD

Universal decay of scalar turbulence

The asymptotic decay of passive scalar fields is solved analytically for the Kraichnan model, where the velocity has a short correlation time. At long times, two universality classes are found, both characterized by a distribution of the scalar -- generally non-Gaussian -- with global self-similar evolution in time. Analogous behavior is found numerically with a more realistic flow resulting from an inverse energy cascade.

nlin.CD

Isotropy vs anisotropy in small-scale turbulence

The decay of large-scale anisotropies in small-scale turbulent flow is investigated. By introducing two different kinds of estimators we discuss the relation between the presence of a hierarchy for the isotropic and the anisotropic scaling exponents and the persistence of anisotropies. Direct measurements from a channel flow numerical simulation are presented.

nlin.CD

Fronts in passive scalar turbulence

The evolution of scalar fields transported by turbulent flow is characterized by the presence of fronts, which rule the small-scale statistics of scalar fluctuations. With the aid of numerical simulations, it is shown that: isotropy is not recovered, in the classical sense, at small scales; scaling exponents are universal with respect to the scalar injection mechanisms; high-order exponents saturate to a constant value; non-mature fronts dominate the statistics of intense fluctuations. Results on the statistics inside the plateaux, where fluctuations are weak, are also presented. Finally, we analyze the statistics of scalar dissipation and scalar fluxes.

nlin.CD

Statistical geometry in scalar turbulence

A general link between geometry and intermittency in passive scalar turbulence is established. Intermittency is qualitatively traced back to events where tracer particles stay for anomalousy long times in degenerate geometries characterized by strong clustering. The quantitative counterpart is the existence of special functions of particle configurations which are statistically invariant under the flow. These are the statistical integrals of motion controlling the scalar statistics at small scales and responsible for the breaking of scale invariance associated to intermittency.

nlin.CD

Universality and saturation of intermittency in passive scalar turbulence

The statistical properties of a scalar field advected by the non-intermittent Navier-Stokes flow arising from a two-dimensional inverse energy cascade are investigated. The universality properties of the scalar field are directly probed by comparing the results obtained with two different types of injection mechanisms. Scaling properties are shown to be universal, even though anisotropies injected at large scales persist down to the smallest scales and local isotropy is not fully restored. Scalar statistics is strongly intermittent and scaling exponents saturate to a constant for sufficiently high orders. This is observed also for the advection by a velocity field rapidly changing in time, pointing to the genericity of the phenomenon. The persistence of anisotropies and the saturation are both statistical signatures of the ramp-and-cliff structures observed in the scalar field.

chao-dyn

Small-scale turbulent dynamo

Kinematic dynamo theory is presented here for turbulent conductive fluids. We describe how inhomogeneous magnetic fluctuations are generated below the viscous scale of turbulence where the spatial smoothness of the velocity permits a systematic analysis of the Lagrangian path dynamics. We find analytically the moments and multi-point correlation functions of the magnetic field at small yet finite magnetic diffusivity. We show that the field is concentrated in long narrow strips and describe anomalous scalings and angular singularities of the multi-point correlation functions which are manifestations of field's intermittency. The growth rate of the magnetic field in a typical realization is found to be half the difference of two Lyapunov exponents of the same sign.

chao-dyn

Inverse cascade in two-dimensional turbulence: deviations from Gaussianity

High resolution numerical simulations of stationary inverse energy cascade in two-dimensional turbulence are presented. Deviations from Gaussianity of velocity differences statistics are quantitatively investigated. The level of statistical convergence is pushed enough to permit reliable measurement of the asymmetries in the probability distribution functions of longitudinal increments and odd-order moments, which bring the signature of the inverse energy flux. Their scaling laws do not present any measurable intermittency correction. The seventh order skewness is found to increase by almost two orders of magnitude with respect to the third, thus becoming of order unity.

chao-dyn

Lagrangian method for multiple correlations in passive scalar advection

A Lagrangian method is introduced for calculating simultaneous n-point correlations of a passive scalar advected by a random velocity field, with random forcing and finite molecular diffusivity kappa. The method, which is here presented in detail, is particularly well suited for studying the kappa tending to 0 limit when the velocity field is not smooth. Efficient Monte Carlo simulations based on this method are applied to the Kraichnan model of passive scalar and lead to accurate determinations of the anomalous intermittency corrections in the fourth-order structure function as a function of the scaling exponent xi of the velocity field in two and three dimensions. Anomalous corrections are found to vanish in the limits xi tending to 0 and xi tending to 2, as predicted by perturbation theory.

cond-mat.stat-mech

Resonant enhanced diffusion in time dependent flow

Explicit examples of scalar enhanced diffusion due to resonances between different transport mechanisms are presented. Their signature is provided by the sharp and narrow peaks observed in the effective diffusivity coefficients and, in the absence of molecular diffusion, by anomalous transport. For the time-dependent flow considered here, resonances arise between their oscillations in time and either molecular diffusion or a mean flow. The effective diffusivities are calculated using multiscale techniques.

chao-dyn