arXiv subjects

B. Mehlig

Publications and source records attributed to B. Mehlig.

At least 73 records · Page 4Linked to original sources

arXiv2016

Inertial-particle accelerations in turbulence: a Lagrangian closure

The distribution of particle accelerations in turbulence is intermittent, with non-Gaussian tails that are quite different for light and heavy particles. In this article we analyse a closure scheme for the acceleration fluctuations of light and heavy inertial particles in turbulence, formulated in terms of Lagrangian correlation functions of fluid tracers. We compute the variance and the flatness of inertial particle accelerations and we discuss their dependency on the Stokes number. The closure incorporates effects induced by the Lagrangian correlations along the trajectories of fluid tracers, and its predictions agree well with results of direct numerical simulations of inertial particles in turbulence, provided that the effects induced by the inertial preferential sampling of heavy/light particles outside/inside vortices are negligible. In particular, the scheme predicts the correct functional behaviour of the acceleration variance, as a function of Stokes, as well as the presence of a minimum/maximum for the flatness of the acceleration of heavy/light particles, in good qualitative agreement with numerical data. We also show that the closure works well when applied to the Lagrangian evolution of particles using a stochastic surrogate for the underlying Eulerian velocity field. Our results support the conclusion that there exist important contributions to the statistics of the acceleration of inertial particles independent of the preferential sampling. For heavy particles we observe deviations between the predictions of the closure scheme and direct numerical simulations, at Stokes numbers of order unity. For light particles the deviation occurs for larger Stokes numbers.

physics.flu-dyn↗

arXiv2016

Statistical model for collisions and recollisions of inertial particles in mixing flows

Finding a quantitative description of the rate of collisions between small particles suspended in mixing flows is a long-standing problem. Here we investigate the validity of a parameterisation of the collision rate for identical particles subject to Stokes force, based on results for relative velocities of heavy particles that were recently obtained within a statistical model for the dynamics of turbulent aerosols. This model represents the turbulent velocity fluctuations by Gaussian random functions. We find that the parameterisation gives quantitatively good results in the limit where the \lq ghost-particle approximation' applies. The collision rate is a sum of two contributions due to \lq caustics' and to \lq clustering'. Within the statistical model we compare the relative importance of these two collision mechanisms. The caustic formation rate is high when the particle inertia becomes large, and we find that caustics dominate the collision rate as soon as they form frequently. We compare the magnitude of the caustic contribution to the collision rate to the formation rate of caustics.

physics.flu-dyn↗

arXiv2016

Preferential sampling and small-scale clustering of gyrotactic microswimmers in turbulence

Recent studies show that spherical motile micro-organisms in turbulence subject to gravitational torques gather in down-welling regions of the turbulent flow. By analysing a statistical model we analytically compute how shape affects the dynamics, preferential sampling, and small-scale spatial clustering. We find that oblong organisms may spend more time in up-welling regions of the flow, and that all organisms are biased to regions of positive fluid-velocity gradients in the upward direction. We analyse small-scale spatial clustering and find that oblong particles may either cluster more or less than spherical ones, depending on the strength of the gravitational torques.

physics.flu-dyn↗

arXiv2016

A universal mechanism generating clusters of differentiated loci during divergence-with-migration

Genome-wide patterns of genetic divergence reveal mechanisms of adaptation under gene flow. Empirical data show that divergence is mostly concentrated in narrow genomic regions. This pattern may arise because differentiated loci protect nearby mutations from gene flow, but recent theory suggests this mechanism is insufficient to explain the emergence of concentrated differentiation during biologically realistic timescales. Critically, earlier theory neglects an inevitable consequence of genetic drift: stochastic loss of local genomic divergence. Here we demonstrate that the rate of stochastic loss of weak local differentiation increases with recombination distance to a strongly diverged locus and, above a critical recombination distance, local loss is faster than local `gain' of new differentiation. Under high migration and weak selection this critical recombination distance is much smaller than the total recombination distance of the genomic region under selection. Consequently, divergence between populations increases by net gain of new differentiation within the critical recombination distance, resulting in tightly-linked clusters of divergence. The mechanism responsible is the balance between stochastic loss and gain of weak local differentiation, a mechanism acting universally throughout the genome. Our results will help to explain empirical observations and lead to novel predictions regarding changes in genomic architectures during adaptive divergence.

q-bio.PE↗

arXiv2016

Nanoconfined circular and linear DNA - equilibrium conformations and unfolding kinetics

Studies of circular DNA confined to nanofluidic channels are relevant both from a fundamental polymer-physics perspective and due to the importance of circular DNA molecules in vivo. We here observe the unfolding of DNA from the circular to linear configuration as a light-induced double strand break occurs, characterize the dynamics, and compare the equilibrium conformational statistics of linear and circular configurations. This is important because it allows us to determine to which extent existing statistical theories describe the extension of confined circular DNA. We find that the ratio of the extensions of confined linear and circular DNA configurations increases as the buffer concentration decreases. The experimental results fall between theoretical predictions for the extended de Gennes regime at weaker confinement and the Odijk regime at stronger confinement. We show that it is possible to directly distinguish between circular and linear DNA molecules by measuring the emission intensity from the DNA. Finally, we determine the rate of unfolding and show that this rate is larger for more confined DNA, possibly reflecting the corresponding larger difference in entropy between the circular and linear configurations.

q-bio.BM↗

arXiv2015

Tumbling of asymmetric microrods in a microchannel flow

We describe results of measurements of the orientational motion of glass microrods in a microchannel flow, following the orientational motion of particles with different shapes. We determine how the orientational dynamics depends on the shape of the particle and on its initial orientation. We find that the dynamics depends so sensitively on the degree to which particle axisymmetry is broken that it is difficult to find particles that are sufficiently axisymmetric so that they exhibit periodic tumbling ("Jeffery orbits"). The results of our measurements confirm earlier theoretical analysis predicting sensitive dependence on particle shape and its initial orientation. Our results illustrate the different types of orientational dynamics for asymmetric particles predicted by theory.

physics.flu-dyn↗

arXiv2015

Numerical analysis of the angular motion of a neutrally buoyant spheroid in shear flow at small Reynolds numbers

We numerically analyse the rotation of a neutrally buoyant spheroid in a shear flow at small shear Reynolds number. Using direct numerical stability analysis of the coupled nonlinear particle-flow problem we compute the linear stability of the log-rolling orbit at small shear Reynolds number, ${\rm Re}_a$. As ${\rm Re}_a \to 0$ and as the box size of the system tends to infinity we find good agreement between the numerical results and earlier analytical predictions valid to linear order in ${\rm Re}_a$ for the case of an unbounded shear. The numerical stability analysis indicates that there are substantial finite-size corrections to the analytical results obtained for the unbounded system. We also compare the analytical results to results of lattice-Boltzmann simulations to analyse the stability of the tumbling orbit at shear Reynolds numbers of order unity. Theory for an unbounded system at infinitesimal shear Reynolds number predicts a bifurcation of the tumbling orbit at aspect ratio $λ_{\rm c} \approx 0.137$ below which tumbling is stable (as well as log rolling). The simulation results show a bifurcation line in the $λ$-${\rm Re}_a$ plane that reaches $λ\approx0.1275$ at the smallest shear Reynolds number (${\rm Re}_a=1$) at which we could simulate with the lattice-Boltzmann code, in qualitative agreement with the analytical results.

physics.flu-dyn↗

arXiv2015

Finite-size corrections for confined polymers in the extended de Gennes regime

Theoretical results for the extension of a polymer confined to a channel are usually derived in the limit of infinite contour length. But experimental studies and simulations of DNA molecules confined to nanochannels are not necessarily in this asymptotic limit. We calculate the statistics of the span and the end-to-end distance of a semiflexible polymer of finite length in the extended de Gennes regime, exploiting the fact that the problem can be mapped to a one-dimensional weakly self-avoiding random walk. The results thus obtained compare favourably with pruned-enriched Rosenbluth method (PERM) simulations of a three-dimensional discrete wormlike chain model of DNA confined in a nanochannel. We discuss the implications for experimental studies of linear $λ$-DNA confined to nanochannels at the high ionic strengths used in many experiments.

cond-mat.soft↗

arXiv2015

Extension of nano-confined DNA: quantitative comparison between experiment and theory

The extension of DNA confined to nanochannels has been studied intensively and in detail. Yet quantitative comparisons between experiments and model calculations are difficult because most theoretical predictions involve undetermined prefactors, and because the model parameters (contour length, Kuhn length, effective width) are difficult to compute reliably, leading to substantial uncertainties. Here we use a recent asymptotically exact theory for the DNA extension in the "extended de Gennes regime" that allows us to compare experimental results with theory. For this purpose we performed new experiments, measuring the mean DNA extension and its standard deviation while varying the channel geometry, dye intercalation ratio, and ionic buffer strength. The experimental results agree very well with theory at high ionic strengths, indicating that the model parameters are reliable. At low ionic strengths the agreement is less good. We discuss possible reasons. Our approach allows, in principle, to measure the Kuhn length and effective width of a single DNA molecule and more generally of semiflexible polymers in solution.

physics.bio-ph↗

arXiv2015

The role of inertia for the rotation of a nearly spherical particle in a general linear flow

We analyse the angular dynamics of a neutrally buoyant nearly spherical particle immersed in a steady general linear flow. The hydrodynamic torque acting on the particle is obtained by means of a reciprocal theorem, regular perturbation theory exploiting the small eccentricity of the nearly spherical particle, and assuming that inertial effects are small, but finite.

physics.flu-dyn↗

arXiv2015

A model for melting of confined DNA

When DNA molecules are heated they denature. This occurs locally so that loops of molten single DNA strands form, connected by intact double-stranded DNA pieces. The properties of this "melting" transition have been intensively investigated. Recently there has been a surge of interest in this question, caused by experiments determining the properties of partially bound DNA confined to nanochannels. But how does such confinement affect the melting transition? To answer this question we introduce, and solve a model predicting how confinement affects the melting transition for a simple model system by first disregarding the effect of self-avoidance. We find that the transition is smoother for narrower channels. By means of Monte-Carlo simulations we then show that a model incorporating self-avoidance shows qualitatively the same behaviour and that the effect of confinement is stronger than in the ideal case.

physics.bio-ph↗

arXiv2015

Effect of weak fluid inertia upon Jeffery orbits

We consider the rotation of small neutrally buoyant axisymmetric particles in a viscous steady shear flow. When inertial effects are negligible the problem exhibits infinitely many periodic solutions, the "Jeffery orbits". We compute how inertial effects lift their degeneracy by perturbatively solving the coupled particle-flow equations. We obtain an equation of motion valid at small shear Reynolds numbers, for spheroidal particles with arbitrary aspect ratios. We analyse how the linear stability of the \lq log-rolling\rq{} orbit depends on particle shape and find it to be unstable for prolate spheroids. This resolves a puzzle in the interpretation of direct numerical simulations of the problem. In general both unsteady and non-linear terms in the Navier-Stokes equations are important.

physics.flu-dyn↗

arXiv2015

Rotation of a spheroid in a simple shear at small Reynolds number

We derive an effective equation of motion for the orientational dynamics of a neutrally buoyant spheroid suspended in a simple shear flow, valid for arbitrary particle aspect ratios and to linear order in the shear Reynolds number. We show how inertial effects lift the degeneracy of the Jeffery orbits and determine the stabilities of the log-rolling and tumbling orbits at infinitesimal shear Reynolds numbers. For prolate spheroids we find stable tumbling in the shear plane, log-rolling is unstable. For oblate particles, by contrast, log-rolling is stable and tumbling is unstable provided that the aspect ratio is larger than a critical value. When the aspect ratio is smaller than this value tumbling turns stable, and an unstable limit cycle is born.

physics.flu-dyn↗

arXiv2015

Entrainment of heterogeneous glycolytic oscillations in single cells

Cell signaling, gene expression, and metabolism are affected by cell-cell heterogeneity and random changes in the environment. The effects of such fluctuations on cell signaling and gene expression have recently been studied intensively using single-cell experiments. In metabolism heterogeneity may be particularly important because it may affect synchronisation of metabolic oscillations, an important example of cell-cell communication. This synchronisation is notoriously difficult to describe theoretically as the example of glycolytic oscillations shows: neither is the mechanism of glycolytic synchronisation understood nor the role of cell-cell heterogeneity. To pin down the mechanism and to assess its robustness and universality we have experimentally investigated the entrainment of glycolytic oscillations in individual yeast cells by periodic external perturbations. We find that oscillatory cells synchronise through phase shifts and that the mechanism is insensitive to cell heterogeneity (robustness) and similar for different types of external perturbations (universality).

physics.bio-ph↗

arXiv2015

Scaling regimes of a semi-flexible polymer in a rectangular channel

We derive scaling relations for the extension statistics and the confinement free energy for a semi-flexible polymer confined to a channel with a rectangular cross-section. Our motivation are recent numerical results [Gupta {\em et al.}, JCP {\bf 140} (2014) 214901] indicating that extensional fluctuations are quite different in rectangular channels compared to square channels. Our results are of direct relevance for interpreting current experiments on DNA molecules confined to nano-channels, as many experiments are performed for rectangular channels with large aspect ratios while theoretical and simulation results are usually obtained for square channels.

cond-mat.soft↗

arXiv2014

Shape-dependence of particle rotation in isotropic turbulence

We consider the rotation of neutrally buoyant axisymmetric particles suspended in isotropic turbulence. Using laboratory experiments as well as numerical and analytical calculations, we explore how particle rotation depends upon particle shape. We find that shape strongly affects orientational trajectories, but that it has negligible effect on the variance of the particle angular velocity. Previous work has shown that shape significantly affects the variance of the tumbling rate of axisymmetric particles. It follows that shape affects the spinning rate in a way that is, on average, complementary to the shape-dependence of the tumbling rate. We confirm this relationship using direct numerical simulations, showing how tumbling rate and spinning rate variances show complementary trends for rod-shaped and disk-shaped particles. We also consider a random but non-turbulent flow. This allows us to explore which of the features observed for rotation in turbulent flow are due to the effects of particle alignment in vortex tubes.

physics.flu-dyn↗

arXiv2014

Confined polymers in the extended de Gennes regime

We show that the problem of describing the conformations of a semiflexible polymer confined to a channel can be mapped onto an exactly solvable model in the so-called extended de Gennes regime. This regime (where the polymer is neither weakly nor strongly confined) has recently been studied intensively experimentally and by means of computer simulations. The exact solution predicts precisely how the conformational fluctuations depend upon the channel width and upon the microscopic parameters characterising the physical properties of the polymer.

cond-mat.soft↗

arXiv2014

Clustering of particles falling in a turbulent flow

Spatial clustering of identical particles falling through a turbulent flow enhances the collision rate between the falling particles, an important problem in aerosol science. We analyse this problem using perturbation theory in a dimensionless parameter, the so-called Kubo number. This allows us to derive an analytical theory quantifying the spatial clustering. We find that clustering of small particles in incompressible random velocity fields may be reduced or enhanced by the effect of gravity (depending on the Stokes number of the particles) and may be strongly anisotropic.

physics.flu-dyn↗