Anisotropic active Brownian particle with a fluctuating propulsion force.

The active Brownian particle (ABP) model describes a swimmer, synthetic or living, whose direction of swimming is a Brownian motion. The swimming is due to a propulsion force, and the fluctuations are typically thermal in origin. We present a two-dimensional model where the fluctuations arise from nonthermal noise in a propelling force acting at a single point, such as that due to a flagellum. We take the overdamped limit and find several modifications to the traditional ABP model. Since the fluctuating force causes a fluctuating torque, the diffusion tensor describing the process has a coupling between translational and rotational degrees of freedom. An anisotropic particle also exhibits a mass-dependent noise-induced drift, which does not disappear in the overdamped limit. We show that these effects have measurable consequences for the long-time diffusivity of active particles, in particular adding a contribution that is independent of where the force acts.

Open-flow mixing and transfer operators.

We study finite-time mixing in time-periodic open flow systems. We describe the transport of densities in terms of a transfer operator, which is represented by the transition matrix of a finite-state Markov chain. The transport processes in the open system are organized by the chaotic saddle and its stable and unstable manifolds. We extract these structures directly from leading eigenvectors of the transition matrix. We use different measures to quantify the degree of mixing and show that they give consistent results in parameter studies of two model systems. This article is part of the theme issue 'Mathematical problems in physical fluid dynamics (part 1)'.

Unravelling hagfish slime.

Hagfish slime is a unique predator defence material containing a network of long fibrous threads each ∼10 cm in length. Hagfish release the threads in a condensed coiled state known as skeins (∼100 µm), which must unravel within a fraction of a second to thwart a predator attack. Here we consider the hypothesis that viscous hydrodynamics can be responsible for this rapid unravelling, as opposed to chemical reaction kinetics alone. Our main conclusion is that, under reasonable physiological conditions, unravelling due to viscous drag can occur within a few hundred milliseconds, and is accelerated if the skein is pinned at a surface such as the mouth of a predator. We model a single skein unspooling as the fibre peels away due to viscous drag. We capture essential features by considering simplified cases of physiologically relevant flows and one-dimensional scenarios where the fibre is aligned with streamlines in either uniform or uniaxial extensional flow. The peeling resistance is modelled with a power-law dependence on peeling velocity. A dimensionless ratio of viscous drag to peeling resistance appears in the dynamical equations and determines the unraveling time scale. Our modelling approach is general and can be refined with future experimental measurements of peel strength for skein unravelling. It provides key insights into the unravelling process, offers potential answers to lingering questions about slime formation from threads and mucous vesicles, and will aid the growing interest in engineering similar bioinspired material systems.

Can phoretic particles swim in two dimensions?

Artificial phoretic particles swim using self-generated gradients in chemical species (self-diffusiophoresis) or charges and currents (self-electrophoresis). These particles can be used to study the physics of collective motion in active matter and might have promising applications in bioengineering. In the case of self-diffusiophoresis, the classical physical model relies on a steady solution of the diffusion equation, from which chemical gradients, phoretic flows, and ultimately the swimming velocity may be derived. Motivated by disk-shaped particles in thin films and under confinement, we examine the extension to two dimensions. Because the two-dimensional diffusion equation lacks a steady state with the correct boundary conditions, Laplace transforms must be used to study the long-time behavior of the problem and determine the swimming velocity. For fixed chemical fluxes on the particle surface, we find that the swimming velocity ultimately always decays logarithmically in time. In the case of finite Péclet numbers, we solve the full advection-diffusion equation numerically and show that this decay can be avoided by the particle moving to regions of unconsumed reactant. Finite advection thus regularizes the two-dimensional phoretic problem.

Distribution of particle displacements due to swimming microorganisms.

The experiments of Leptos et al. [Phys. Rev. Lett. 103, 198103 (2009)] show that the displacements of small particles affected by swimming microorganisms achieve a non-Gaussian distribution, which nevertheless scales diffusively--the "diffusive scaling." We use a simple model where the particles undergo repeated "kicks" due to the swimmers to explain the shape of the distribution as a function of the volume fraction of swimmers. The net displacement is determined by the inverse Fourier transform of a single-swimmer characteristic function. The only adjustable parameter is the strength of the stresslet term in our spherical squirmer model. We give a criterion for convergence to a Gaussian distribution in terms of moments of the drift function and show that the experimentally observed diffusive scaling is a transient related to the slow crossover of the fourth moment from a ballistic to a linear regime with path length. We also present a simple model, with logarithmic drift function, that can be solved analytically.

Finite-time braiding exponents.

Topological entropy of a dynamical system is an upper bound for the sum of positive Lyapunov exponents; in practice, it is strongly indicative of the presence of mixing in a subset of the domain. Topological entropy can be computed by partition methods, by estimating the maximal growth rate of material lines or other material elements, or by counting the unstable periodic orbits of the flow. All these methods require detailed knowledge of the velocity field that is not always available, for example, when ocean flows are measured using a small number of floating sensors. We propose an alternative calculation, applicable to two-dimensional flows, that uses only a sparse set of flow trajectories as its input. To represent the sparse set of trajectories, we use braids, algebraic objects that record how trajectories exchange positions with respect to a projection axis. Material curves advected by the flow are represented as simplified loop coordinates. The exponential rate at which a braid stretches loops over a finite time interval is the Finite-Time Braiding Exponent (FTBE). We study FTBEs through numerical simulations of the Aref Blinking Vortex flow, as a representative of a general class of flows having a single invariant component with positive topological entropy. The FTBEs approach the value of the topological entropy from below as the length and number of trajectories is increased; we conjecture that this result holds for a general class of ergodic, mixing systems. Furthermore, FTBEs are computed robustly with respect to the numerical time step, details of braid representation, and choice of initial conditions. We find that, in the class of systems we describe, trajectories can be re-used to form different braids, which greatly reduces the amount of data needed to assess the complexity of the flow.

Moving walls accelerate mixing.

Mixing in viscous fluids is challenging, but chaotic advection in principle allows efficient mixing. In the best possible scenario, the decay rate of the concentration profile of a passive scalar should be exponential in time. In practice, several authors have found that the no-slip boundary condition at the walls of a vessel can slow down mixing considerably, turning an exponential decay into a power law. This slowdown affects the whole mixing region, and not just the vicinity of the wall. The reason is that when the chaotic mixing region extends to the wall, a separatrix connects to it. The approach to the wall along that separatrix is polynomial in time and dominates the long-time decay. However, if the walls are moved or rotated, closed orbits appear, separated from the central mixing region by a hyperbolic fixed point with a homoclinic orbit. The long-time approach to the fixed point is exponential, so an overall exponential decay is recovered, albeit with a thin unmixed region near the wall.

Braids of entangled particle trajectories.

In many applications, the two-dimensional trajectories of fluid particles are available, but little is known about the underlying flow. Oceanic floats are a clear example. To extract quantitative information from such data, one can measure single-particle dispersion coefficients, but this only uses one trajectory at a time, so much of the information on relative motion is lost. In some circumstances the trajectories happen to remain close long enough to measure finite-time Lyapunov exponents, but this is rare. We propose to use tools from braid theory and the topology of surface mappings to approximate the topological entropy of the underlying flow. The procedure uses all the trajectory data and is inherently global. The topological entropy is a measure of the entanglement of the trajectories, and converges to zero if they are not entangled in a complex manner (for instance, if the trajectories are all in a large vortex). We illustrate the techniques on some simple dynamical systems and on float data from the Labrador Sea. The method could eventually be used to identify Lagrangian coherent structures present in the flow.

Topology of chaotic mixing patterns.

A stirring device consisting of a periodic motion of rods induces a mapping of the fluid domain to itself, which can be regarded as a homeomorphism of a punctured surface. Having the rods undergo a topologically complex motion guarantees at least a minimal amount of stretching of material lines, which is important for chaotic mixing. We use topological considerations to describe the nature of the injection of unmixed material into a central mixing region, which takes place at injection cusps. A topological index formula allow us to predict the possible types of unstable foliations that can arise for a fixed number of rods.

Dynamical effects and phase separation in cooled binary fluid films.

We study phase separation in thin films using a model based on the Navier-Stokes Cahn-Hilliard equations in the lubrication approximation, with a van der Waals potential to account for substrate-film interactions. We solve the resulting thin-film equations numerically and compare to experimental data. The model captures the qualitative features of real phase-separating fluids, in particular, how concentration gradients produce film thinning and surface roughening. The ultimate outcome of the phase separation depends strongly on the dynamical back reaction of concentration gradients on the flow, an effect we demonstrate by applying a shear stress at the film's surface. When the back reaction is small, the phase domain boundaries align with the direction of the imposed stress, while for larger back-reaction strengths, the domains align in the perpendicular direction.

Bubbles and filaments: stirring a Cahn-Hilliard fluid.

The advective Cahn-Hilliard equation describes the competing processes of stirring and separation in a two-phase fluid. Intuition suggests that bubbles will form on a certain scale, and previous studies of Cahn-Hilliard dynamics seem to suggest the presence of one dominant length scale. However, the Cahn-Hilliard phase-separation mechanism contains a hyperdiffusion term and we show that, by stirring the mixture at a sufficiently large amplitude, we excite the diffusion and overwhelm the segregation to create a homogeneous liquid. At intermediate amplitudes we see regions of bubbles coexisting with regions of hyperdiffusive filaments. Thus, the problem possesses two dominant length scales, associated with the bubbles and filaments. For simplicity, we use a chaotic flow that mimics turbulent stirring at large Prandtl number. We compare our results with the case of variable mobility, in which growth of bubble size is dominated by interfacial rather than bulk effects, and find qualitatively similar results.

Topology, braids and mixing in fluids.

Stirring of fluid with moving rods is necessary in many practical applications to achieve homogeneity. These rods are topological obstacles that force stretching of fluid elements. The resulting stretching and folding is commonly observed as filaments and striations, and is a precursor to mixing. In a space-time diagram, the trajectories of the rods form a braid, and the properties of this braid impose a minimal complexity in the flow. We review the topological viewpoint of fluid mixing, and discuss how braids can be used to diagnose mixing and construct efficient mixing devices. We introduce a new, realizable design for a mixing device, the silver mixer, based on these principles.

Multiscale mixing efficiencies for steady sources.

Multiscale mixing efficiencies for passive scalar advection are defined in terms of the suppression of variance weighted at various length scales. We consider scalars maintained by temporally steady but spatially inhomogeneous sources, stirred by statistically homogeneous and isotropic incompressible flows including fully developed turbulence. The mixing efficiencies are rigorously bounded in terms of the Péclet number and specific quantitative features of the source. Scaling exponents for the bounds at high Péclet number depend on the spectrum of length scales in the source, indicating that molecular diffusion plays a more important quantitative role than that implied by classical eddy diffusion theories.

Topological mixing with ghost rods.

Topological chaos relies on the periodic motion of obstacles in a two-dimensional flow in order to form nontrivial braids. This motion generates exponential stretching of material lines, and hence efficient mixing. Boyland, Aref, and Stremler [J. Fluid Mech. 403, 277 (2000)] have studied a specific periodic motion of rods that exhibits topological chaos in a viscous fluid. We show that it is possible to extend their work to cases where the motion of the stirring rods is topologically trivial by considering the dynamics of special periodic points that we call "ghost rods", because they play a similar role to stirring rods. The ghost rods framework provides a new technique for quantifying chaos and gives insight into the mechanisms that produce chaos and mixing. Numerical simulations for Stokes flow support our results.

Measuring topological chaos.

The orbits of fluid particles in two dimensions effectively act as topological obstacles to material lines. A spacetime plot of the orbits of such particles can be regarded as a braid whose properties reflect the underlying dynamics. For a chaotic flow, the braid generated by the motion of three or more fluid particles is computed. A "braiding exponent" is then defined to characterize the complexity of the braid. This exponent is proportional to the usual Lyapunov exponent of the flow, associated with separation of nearby trajectories. Measuring chaos in this manner has several advantages, especially from the experimental viewpoint, since neither nearby trajectories nor derivatives of the velocity field are needed.

The strange eigenmode in Lagrangian coordinates.

For a distribution advected by a simple chaotic map with diffusion, the "strange eigenmode" is investigated from the Lagrangian (material) viewpoint and compared to its Eulerian (spatial) counterpart. The eigenmode embodies the balance between diffusion and exponential stretching by a chaotic flow. It is not strictly an eigenmode in Lagrangian coordinates, because its spectrum is rescaled exponentially rapidly.

Chaotic mixing in a torus map.

The advection and diffusion of a passive scalar is investigated for a map of the 2-torus. The map is chaotic, and the limit of almost-uniform stretching is considered. This allows an analytic understanding of the transition from a phase of constant scalar variance (for short times) to exponential decay (for long times). This transition is embodied in a short superexponential phase of decay. The asymptotic state in the exponential phase is an eigenfunction of the advection-diffusion operator, in which most of the scalar variance is concentrated at small scales, even though a large-scale mode sets the decay rate. The duration of the superexponential phase is proportional to the logarithm of the exponential decay rate; if the decay is slow enough then there is no superexponential phase at all.

Geometrical constraints on finite-time Lyapunov exponents in two and three dimensions.

Constraints are found on the spatial variation of finite-time Lyapunov exponents of two- and three-dimensional systems of ordinary differential equations. In a chaotic system, finite-time Lyapunov exponents describe the average rate of separation, along characteristic directions, of neighboring trajectories. The solution of the equations is a coordinate transformation that takes initial conditions (the Lagrangian coordinates) to the state of the system at a later time (the Eulerian coordinates). This coordinate transformation naturally defines a metric tensor, from which the Lyapunov exponents and characteristic directions are obtained. By requiring that the Riemann curvature tensor vanish for the metric tensor (a basic result of differential geometry in a flat space), differential constraints relating the finite-time Lyapunov exponents to the characteristic directions are derived. These constraints are realized with exponential accuracy in time. A consequence of the relations is that the finite-time Lyapunov exponents are locally small in regions where the curvature of the stable manifold is large, which has implications for the efficiency of chaotic mixing in the advection-diffusion equation. The constraints also modify previous estimates of the asymptotic growth rates of quantities in the dynamo problem, such as the magnitude of the induced current. (c) 2001 American Institute of Physics.