Lagrangian based methods for coherent structure detection

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.

Spectral-Clustering of Lagrangian Trajectory Graphs: Application to Abdominal Aortic Aneurysms

PURPOSE

Identification of coherent structures in cardiovascular flows is crucial to describe the transport and mixing of blood. Coherent structures can highlight locations where minimal blood mixing takes place, thus, potential thrombus formation can be expected thither. Graph-based approaches have recently been introduced in order to describe fluid transport and mixing between multiple Lagrangian trajectories, where each trajectory serves as a node that can be connected to another trajectory based on their relative distance during the course of time.

METHODS

In this study, we compute the Lagrangian trajectories from in vitro planar instantaneous velocity fields in two models of abdominal aortic aneurysms, (AAA) namely single bulge and bi-lobed. Then, we construct unweighted and undirected graphs based on the pairwise distance of Lagrangian trajectories. We report local measures of the graph namely the degree and the clustering coefficient. We also perform spectral clustering of the graph Laplacian to extract the flow coherent sets.

RESULTS

Local graph measures reveal fluid regions of high mixing such as vortex boundaries. Through spectral clustering, the fluid is partitioned into a reduced number of coherent sets where within each set, inner mixing of fluid is maximized while the fluid mixing between different coherent sets is minimized. The approach reveals multiple coherent sets adjacent to the AAA bulge that have sustained this adjacency to the wall through their coherent motion during one cardiac cycle.

CONCLUSION

Identifying coherent sets enables tracking their transport during the cardiac cycle and identify their role in the flow dynamics. Moreover, the size and the transport of the long residing coherent sets inside the AAA bulges can be deduced which may aid in predicting thrombus formation at such location.

Detection of functional communities in networks of randomly coupled oscillators using the dynamic-mode decomposition

Dynamic-mode decomposition (DMD) is a versatile framework for model-free analysis of time series that are generated by dynamical systems. We develop a DMD-based algorithm to investigate the formation of functional communities in networks of coupled, heterogeneous Kuramoto oscillators. In these functional communities, the oscillators in a network have similar dynamics. We consider two common random-graph models (Watts-Strogatz networks and Barabási-Albert networks) with different amounts of heterogeneities among the oscillators. In our computations, we find that membership in a functional community reflects the extent to which there is establishment and sustainment of locking between oscillators. We construct forest graphs that illustrate the complex ways in which the heterogeneous oscillators associate and disassociate with each other.

Lower Thermospheric Material Transport via Lagrangian Coherent Structures

We show that inter-model variation due to under-constraint by observations impacts the ability to predict material transport in the lower thermosphere. Lagrangian coherent structures (LCSs), indicating regions of maximal separation (or convergence) in a time-varying flow, are derived in the lower thermosphere from models for several space shuttle water vapor plume events. We find that inter-model differences in thermospheric transport manifest in LCSs in a way that is more stringent than mean wind analyses. LCSs defined using horizontal flow fields from the Specified Dynamics version of the Whole Atmosphere Community Climate Model with thermosphere-ionosphere eXtension (SD-WACCMX) at 109 km altitude are compared to Global Ultraviolet Imager (GUVI) observations of the space shuttle main engine plume. In one case, SD-WACCMX predicts an LCS ridge to produce spreading not found in the observations. LCSs and tracer transport from SD-WACCMX and from data assimilative WACCMX (WACCMX + DART) are compared to each other and to GUVI observations. Differences in the modeled LCSs and tracer positions appear between SD-WACCMX and WACCMX + DART despite the similarity of mean winds. WACCMX + DART produces better tracer transport results for a July 2006 event, but it is unclear which model performs better in terms of LCS ridges. For a February 2010 event, when mean winds differ by up to 50 m/s between the models, differences in LCSs and tracer trajectories are even more severe. Low-pass filtering the winds up to zonal wavenumber 6 reduces but does not eliminate inter-model LCS differences. Inter-model alignment of LCSs improves at a lower 60 km altitude.

Lower Thermospheric Material Transport via Lagrangian Coherent Structures

We show that inter-model variation due to under-constraint by observations impacts the ability to predict material transport in the lower thermosphere. Lagrangian coherent structures (LCSs), indicating regions of maximal separation (or convergence) in a time-varying flow, are derived in the lower thermosphere from models for several space shuttle water vapor plume events. We find that inter-model differences in thermospheric transport manifest in LCSs in a way that is more stringent than mean wind analyses. LCSs defined using horizontal flow fields from the Specified Dynamics version of the Whole Atmosphere Community Climate Model with thermosphere-ionosphere eXtension (SD-WACCMX) at 109 km altitude are compared to Global Ultraviolet Imager (GUVI) observations of the space shuttle main engine plume. In one case, SD-WACCMX predicts an LCS ridge to produce spreading not found in the observations. LCSs and tracer transport from SD-WACCMX and from data assimilative WACCMX (WACCMX + DART) are compared to each other and to GUVI observations. Differences in the modeled LCSs and tracer positions appear between SD-WACCMX and WACCMX + DART despite the similarity of mean winds. WACCMX + DART produces better tracer transport results for a July 2006 event, but it is unclear which model performs better in terms of LCS ridges. For a February 2010 event, when mean winds differ by up to 50 m/s between the models, differences in LCSs and tracer trajectories are even more severe. Low-pass filtering the winds up to zonal wavenumber 6 reduces but does not eliminate inter-model LCS differences. Inter-model alignment of LCSs improves at a lower 60 km altitude.

An Optimized-Parameter Spectral Clustering Approach to Coherent Structure Detection in Geophysical Flows

In Lagrangian dynamics, the detection of coherent clusters can help understand the organization of transport by identifying regions with coherent trajectory patterns. Many clustering algorithms, however, rely on user-input parameters, requiring a priori knowledge about the flow and making the outcome subjective. Building on the conventional spectral clustering method of Hadjighasem et al. (2016), a new optimized-parameter spectral clustering approach is developed that automatically identifies optimal parameters within pre-defined ranges. A noise-based metric for quantifying the coherence of the resulting coherent clusters is also introduced. The optimized-parameter spectral clustering is applied to two benchmark analytical flows, the Bickley Jet and the asymmetric Duffing oscillator, and to a realistic, numerically generated oceanic coastal flow. In the latter case, the identified model-based clusters are tested using observed trajectories of real drifters. In all examples, our approach succeeded in performing the partition of the domain into coherent clusters with minimal inter-cluster similarity and maximum intra-cluster similarity. For the coastal flow, the resulting coherent clusters are qualitatively similar over the same phase of the tide on different days and even different years, whereas coherent clusters for the opposite tidal phase are qualitatively different.

Material coherence from trajectories via Burau eigenanalysis of braids

In this paper, we provide a numerical tool to study a material's coherence from a set of 2D Lagrangian trajectories sampling a dynamical system, i.e., from the motion of passive tracers. We show that eigenvectors of the Burau representation of a topological braid derived from the trajectories have levelsets corresponding to components of the Nielsen-Thurston decomposition of the dynamical system. One can thus detect and identify clusters of space-time trajectories corresponding to coherent regions of the dynamical system by solving an eigenvalue problem. Unlike previous methods, the scalable computational complexity of our braid-based approach allows the analysis of large amounts of trajectories.

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.

Kernel methods for detecting coherent structures in dynamical data

We illustrate relationships between classical kernel-based dimensionality reduction techniques and eigendecompositions of empirical estimates of reproducing kernel Hilbert space operators associated with dynamical systems. In particular, we show that kernel canonical correlation analysis (CCA) can be interpreted in terms of kernel transfer operators and that it can be obtained by optimizing the variational approach for Markov processes score. As a result, we show that coherent sets of particle trajectories can be computed by kernel CCA. We demonstrate the efficiency of this approach with several examples, namely, the well-known Bickley jet, ocean drifter data, and a molecular dynamics problem with a time-dependent potential. Finally, we propose a straightforward generalization of dynamic mode decomposition called coherent mode decomposition. Our results provide a generic machine learning approach to the computation of coherent sets with an objective score that can be used for cross-validation and the comparison of different methods.

Observability of laminar bidimensional fluid flows seen as autonomous chaotic systems

Lagrangian transport in the dynamical systems approach has so far been investigated disregarding the connection between the whole state space and the concept of observability. Key issues such as the definitions of Lagrangian and chaotic mixing are revisited under this light, establishing the importance of rewriting nonautonomous flow systems derived from a stream function in autonomous form, and of not restricting the characterization of their dynamics in subspaces. The observability of Lagrangian chaos from a reduced set of measurements is illustrated with two canonical examples: the Lorenz system derived as a low-dimensional truncation of the Rayleigh-Bénard convection equations and the driven double-gyre system introduced as a kinematic model of configurations observed in the ocean. A symmetrized version of the driven double-gyre model is proposed.

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.

Simultaneous coherent structure coloring facilitates interpretable clustering of scientific data by amplifying dissimilarity

The clustering of data into physically meaningful subsets often requires assumptions regarding the number, size, or shape of the subgroups. Here, we present a new method, simultaneous coherent structure coloring (sCSC), which accomplishes the task of unsupervised clustering without a priori guidance regarding the underlying structure of the data. sCSC performs a sequence of binary splittings on the dataset such that the most dissimilar data points are required to be in separate clusters. To achieve this, we obtain a set of orthogonal coordinates along which dissimilarity in the dataset is maximized from a generalized eigenvalue problem based on the pairwise dissimilarity between the data points to be clustered. This sequence of bifurcations produces a binary tree representation of the system, from which the number of clusters in the data and their interrelationships naturally emerge. To illustrate the effectiveness of the method in the absence of a priori assumptions, we apply it to three exemplary problems in fluid dynamics. Then, we illustrate its capacity for interpretability using a high-dimensional protein folding simulation dataset. While we restrict our examples to dynamical physical systems in this work, we anticipate straightforward translation to other fields where existing analysis tools require ad hoc assumptions on the data structure, lack the interpretability of the present method, or in which the underlying processes are less accessible, such as genomics and neuroscience.

Ensemble-based topological entropy calculation (E-tec)

Topological entropy measures the number of distinguishable orbits in a dynamical system, thereby quantifying the complexity of chaotic dynamics. One approach to computing topological entropy in a two-dimensional space is to analyze the collective motion of an ensemble of system trajectories taking into account how trajectories "braid" around one another. In this spirit, we introduce the Ensemble-based Topological Entropy Calculation, or E-tec, a method to derive a lower-bound on topological entropy of two-dimensional systems by considering the evolution of a "rubber band" (piece-wise linear curve) wrapped around the data points and evolving with their trajectories. The topological entropy is bounded below by the exponential growth rate of this band. We use tools from computational geometry to track the evolution of the rubber band as data points strike and deform it. Because we maintain information about the configuration of trajectories with respect to one another, updating the band configuration is performed locally, which allows E-tec to be more computationally efficient than some competing methods. In this work, we validate and illustrate many features of E-tec on a chaotic lid-driven cavity flow. In particular, we demonstrate convergence of E-tec's approximation with respect to both the number of trajectories (ensemble size) and the duration of trajectories in time.

Local causal states and discrete coherent structures

Coherent structures form spontaneously in nonlinear spatiotemporal systems and are found at all spatial scales in natural phenomena from laboratory hydrodynamic flows and chemical reactions to ocean, atmosphere, and planetary climate dynamics. Phenomenologically, they appear as key components that organize the macroscopic behaviors in such systems. Despite a century of effort, they have eluded rigorous analysis and empirical prediction, with progress being made only recently. As a step in this, we present a formal theory of coherent structures in fully discrete dynamical field theories. It builds on the notion of structure introduced by computational mechanics, generalizing it to a local spatiotemporal setting. The analysis' main tool employs the local causal states, which are used to uncover a system's hidden spatiotemporal symmetries and which identify coherent structures as spatially localized deviations from those symmetries. The approach is behavior-driven in the sense that it does not rely on directly analyzing spatiotemporal equations of motion, rather it considers only the spatiotemporal fields a system generates. As such, it offers an unsupervised approach to discover and describe coherent structures. We illustrate the approach by analyzing coherent structures generated by elementary cellular automata, comparing the results with an earlier, dynamic-invariant-set approach that decomposes fields into domains, particles, and particle interactions.

Optimal stretching in the reacting wake of a bluff body

We experimentally study spreading of the Belousov-Zhabotinsky reaction behind a bluff body in a laminar flow. Locations of reacted regions (i.e., regions with high product concentration) correlate with a moderate range of Lagrangian stretching and that range is close to the range of optimal stretching previously observed in topologically different flows [T. D. Nevins and D. H. Kelley, Phys. Rev. Lett. 117, 164502 (2016)]. The previous work found optimal stretching in a closed, vortex dominated flow, but this article uses an open flow and only a small area of appreciable vorticity. We hypothesize that optimal stretching is common in advection-reaction-diffusion systems with an excitation threshold, including excitable and bistable systems, and that the optimal range depends on reaction chemistry and not on flow shape or characteristic speed. Our results may also give insight into plankton blooms behind islands in ocean currents.

Identification of individual coherent sets associated with flow trajectories using coherent structure coloring

We present a method for identifying the coherent structures associated with individual Lagrangian flow trajectories even where only sparse particle trajectory data are available. The method, based on techniques in spectral graph theory, uses the Coherent Structure Coloring vector and associated eigenvectors to analyze the distance in higher-dimensional eigenspace between a selected reference trajectory and other tracer trajectories in the flow. By analyzing this distance metric in a hierarchical clustering, the coherent structure of which the reference particle is a member can be identified. This algorithm is proven successful in identifying coherent structures of varying complexities in canonical unsteady flows. Additionally, the method is able to assess the relative coherence of the associated structure in comparison to the surrounding flow. Although the method is demonstrated here in the context of fluid flow kinematics, the generality of the approach allows for its potential application to other unsupervised clustering problems in dynamical systems such as neuronal activity, gene expression, or social networks.

A critical comparison of Lagrangian methods for coherent structure detection

We review and test twelve different approaches to the detection of finite-time coherent material structures in two-dimensional, temporally aperiodic flows. We consider both mathematical methods and diagnostic scalar fields, comparing their performance on three benchmark examples: the quasiperiodically forced Bickley jet, a two-dimensional turbulence simulation, and an observational wind velocity field from Jupiter's atmosphere. A close inspection of the results reveals that the various methods often produce very different predictions for coherent structures, once they are evaluated beyond heuristic visual assessment. As we find by passive advection of the coherent set candidates, false positives and negatives can be produced even by some of the mathematically justified methods due to the ineffectiveness of their underlying coherence principles in certain flow configurations. We summarize the inferred strengths and weaknesses of each method, and make general recommendations for minimal self-consistency requirements that any Lagrangian coherence detection technique should satisfy.

Understanding the geometry of transport: Diffusion maps for Lagrangian trajectory data unravel coherent sets

Dynamical systems often exhibit the emergence of long-lived coherent sets, which are regions in state space that keep their geometric integrity to a high extent and thus play an important role in transport. In this article, we provide a method for extracting coherent sets from possibly sparse Lagrangian trajectory data. Our method can be seen as an extension of diffusion maps to trajectory space, and it allows us to construct "dynamical coordinates," which reveal the intrinsic low-dimensional organization of the data with respect to transport. The only a priori knowledge about the dynamics that we require is a locally valid notion of distance, which renders our method highly suitable for automated data analysis. We show convergence of our method to the analytic transfer operator framework of coherence in the infinite data limit and illustrate its potential on several two- and three-dimensional examples as well as real world data.

Dynamics and transport properties of three surface quasigeostrophic point vortices

The surface quasi-geostrophic (SQG) equations are a model for low-Rossby number geophysical flows in which the dynamics are governed by potential temperature dynamics on the boundary. We examine point vortex solutions to this model as well as the chaotic flows induced by three point vortices. The chaotic transport induced by these flows is investigated using techniques of Poincaré maps and the Finite Time Braiding Exponent (FTBE). This chaotic transport is representative of the mixing in the flow, and these terms are used interchangeably in this work. Compared with point vortices in two-dimensional flow, the SQG vortices are found to produce flows with higher FTBE, indicating more mixing. Select results are presented for analyzing mixing for arbitrary vortex strengths.

Optimal Stretching in Advection-Reaction-Diffusion Systems

We investigate growth of the excitable Belousov-Zhabotinsky reaction in chaotic, time-varying flows. In slow flows, reacted regions tend to lie near vortex edges, whereas fast flows restrict reacted regions to vortex cores. We show that reacted regions travel toward vortex centers faster as flow speed increases, but nonreactive scalars do not. For either slow or fast flows, reaction is promoted by the same optimal range of the local advective stretching, but stronger stretching causes reaction blowout and can hinder reaction from spreading. We hypothesize that optimal stretching and blowout occur in many advection-diffusion-reaction systems, perhaps creating ecological niches for phytoplankton in the ocean.

Effect of the vertical component of diffusion on passive scalar transport in an isolated vortex model

On the basis of the ellipsoidal vortex model and a Monte-Carlo-type diffusion simulation, we examine the flux and ensuing distribution of passive fluid particles through the boundary of an idealized geophysical vortex. Our focus is on features that the horizontal and vertical diffusion components introduce into the fluid particle transport. We examine the concurrent effect of both components, and we compare it with the only horizontal diffusion impact. We analyze the ellipsoid vortex model in two cases: (i) the steady state when the ellipsoid is motionless, i.e., there is no variation in its axes' lengths, and consequently the exterior fluid is not being stirred; (ii) the perturbed case when the ellipsoid rotates periodically, varying it axes' lengths, which results in the appearance of stirred fluid outside the ellipsoid. Influenced by diffusion, a fluid particle is now permitted to move to another vertical horizon, thus there is an increased possibility that the particle will eventually be located in the exterior stirred region rather than in the ellipsoid vortex with the regular dynamics. This is because the area of the horizontal section of the ellipsoid vortex decreases with depth, but the region of stirred exterior fluid extends significantly deeper. Numerical calculations show that factoring in the vertical component of diffusion significantly affects scalar spreading in the horizontal plane in the perturbed case, while in the steady state the vertical component of diffusion only induces dispersion linear growth according to a Gaussian distribution.