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)'.

Evolutionary clustering of Lagrangian trajectories in turbulent Rayleigh-Bénard convection flows.

We explore the transport mechanisms of heat in two- and three-dimensional turbulent convection flows by means of the long-term evolution of Lagrangian coherent sets. They are obtained from the spectral clustering of trajectories of massless fluid tracers that are advected in the flow. Coherent sets result from trajectories that stay closely together under the dynamics of the turbulent flow. For longer times, they are always destroyed by the intrinsic turbulent dispersion of material transport. Here, this constraint is overcome by the application of evolutionary clustering algorithms that add a time memory to the coherent set detection and allows individual trajectories to leak in or out of evolving clusters. Evolutionary clustering thus also opens the possibility to monitor the splits and mergers of coherent sets. These rare dynamic events leave clear footprints in the evolving eigenvalue spectrum of the Laplacian matrix of the trajectory network in both convection flows. The Lagrangian trajectories reveal the individual pathways of convective heat transfer across the fluid layer. We identify the long-term coherent sets as those fluid flow regions that contribute least to heat transfer. Thus, our evolutionary framework defines a complementary perspective on the slow dynamics of turbulent superstructure patterns in convection flows that were recently discussed in the Eulerian frame of reference. The presented framework might be well suited for studies in natural flows, which are typically based on sparse information from drifters and probes.

Network measures of mixing.

Transport and mixing processes in fluid flows can be studied directly from Lagrangian trajectory data, such as those obtained from particle tracking experiments. Recent work in this context highlights the application of graph-based approaches, where trajectories serve as nodes and some similarity or distance measure between them is employed to build a (possibly weighted) network, which is then analyzed using spectral methods. Here, we consider the simplest case of an unweighted, undirected network and analytically relate local network measures such as node degree or clustering coefficient to flow structures. In particular, we use these local measures to divide the family of trajectories into groups of similar dynamical behavior via manifold learning methods.

Molecular crowding creates traffic jams of kinesin motors on microtubules.

Despite the crowdedness of the interior of cells, microtubule-based motor proteins are able to deliver cargoes rapidly and reliably throughout the cytoplasm. We hypothesize that motor proteins may be adapted to operate in crowded environments by having molecular properties that prevent them from forming traffic jams. To test this hypothesis, we reconstituted high-density traffic of purified kinesin-8 motor protein, a highly processive motor with long end-residency time, along microtubules in a total internal-reflection fluorescence microscopy assay. We found that traffic jams, characterized by an abrupt increase in the density of motors with an associated abrupt decrease in motor speed, form even in the absence of other obstructing proteins. To determine the molecular properties that lead to jamming, we altered the concentration of motors, their processivity, and their rate of dissociation from microtubule ends. Traffic jams occurred when the motor density exceeded a critical value (density-induced jams) or when motor dissociation from the microtubule ends was so slow that it resulted in a pileup (bottleneck-induced jams). Through comparison of our experimental results with theoretical models and stochastic simulations, we characterized in detail under which conditions density- and bottleneck-induced traffic jams form or do not form. Our results indicate that transport kinesins, such as kinesin-1, may be evolutionarily adapted to avoid the formation of traffic jams by moving only with moderate processivity and dissociating rapidly from microtubule ends.

A rough-and-ready cluster-based approach for extracting finite-time coherent sets from sparse and incomplete trajectory data.

We present a numerical method to identify regions of phase space that are approximately retained in a mobile compact neighbourhood over a finite time duration. Our approach is based on spatio-temporal clustering of trajectory data. The main advantages of the approach are the ability to produce useful results (i) when there are relatively few trajectories and (ii) when there are gaps in observation of the trajectories as can occur with real data. The method is easy to implement, works in any dimension, and is fast to run.

Lagrangian coherent sets in turbulent Rayleigh-Bénard convection.

Coherent circulation rolls and their relevance for the turbulent heat transfer in a two-dimensional Rayleigh-Bénard convection model are analyzed. The flow is in a closed cell of aspect ratio four at a Rayleigh number Ra=10^{6} and at a Prandtl number Pr=10. Three different Lagrangian analysis techniques based on graph Laplacians (distance spectral trajectory clustering, time-averaged diffusion maps, and finite-element based dynamic Laplacian discretization) are used to monitor the turbulent fields along trajectories of massless Lagrangian particles in the evolving turbulent convection flow. The three methods are compared to each other and the obtained coherent sets are related to results from an analysis in the Eulerian frame of reference. We show that the results of these methods agree with each other and that Lagrangian and Eulerian coherent sets form basically a disjoint union of the flow domain. Additionally, a windowed time averaging of variable interval length is performed to study the degree of coherence as a function of this additional coarse graining which removes small-scale fluctuations that cause trajectories to disperse quickly. Finally, the coherent set framework is extended to study heat transport.

Role of critical points of the skin friction field in formation of plumes in thermal convection.

The dynamics in the thin boundary layers of temperature and velocity is the key to a deeper understanding of turbulent transport of heat and momentum in thermal convection. The velocity gradient at the hot and cold plates of a Rayleigh-Bénard convection cell forms the two-dimensional skin friction field and is related to the formation of thermal plumes in the respective boundary layers. Our analysis is based on a direct numerical simulation of Rayleigh-Bénard convection in a closed cylindrical cell of aspect ratio Γ=1 and focused on the critical points of the skin friction field. We identify triplets of critical points, which are composed of two unstable nodes and a saddle between them, as the characteristic building block of the skin friction field. Isolated triplets as well as networks of triplets are detected. The majority of the ridges of linelike thermal plumes coincide with the unstable manifolds of the saddles. From a dynamical Lagrangian perspective, thermal plumes are formed together with an attractive hyperbolic Lagrangian coherent structure of the skin friction field. We also discuss the differences from the skin friction field in turbulent channel flows from the perspective of the Poincaré-Hopf index theorem for two-dimensional vector fields.

Accurate control of hyperbolic trajectories in any dimension.

The unsteady (nonautonomous) analog of a hyperbolic fixed point is a hyperbolic trajectory, whose importance is underscored by its attached stable and unstable manifolds, which have relevance in fluid flow barriers, chaotic basin boundaries, and the long-term behavior of the system. We develop a method for obtaining the unsteady control velocity which forces a hyperbolic trajectory to follow a user-prescribed variation with time. Our method is applicable in any dimension, and accuracy to any order is achievable. We demonstrate and validate our method by (1) controlling the fixed point at the origin of the Lorenz system, for example, obtaining a user-defined nonautonomous attractor, and (2) the saddle points in a droplet flow, using localized control which generates global transport.