Chaotic advection, diffusion, and reactions in open flows

Fractal structures in the chaotic advection of passive scalars in leaky planar hydrodynamical flows

The advection of passive scalars in time-independent two-dimensional incompressible fluid flows is an integrable Hamiltonian system. It becomes non-integrable if the corresponding stream function depends explicitly on time, allowing the possibility of chaotic advection of particles. We consider for a specific model (double gyre flow), a given number of exits through which advected particles can leak, without disturbing the flow itself. We investigate fractal escape basins in this problem and characterize fractality by computing the uncertainty exponent and basin entropy. Furthermore, we observe the presence of basin boundaries with points exhibiting the Wada property, i.e., boundary points that separate three or more escape basins.

Transport of blood particles: Chaotic advection even in a healthy scenario

We study the advection of blood particles in the carotid bifurcation, a site that is prone to plaque development. Previously, it has been shown that chaotic advection can take place in blood flows with diseases. Here, we show that even in a healthy scenario, chaotic advection can take place. To understand how the particle dynamics is affected by the emergence and growth of a plaque, we study the carotid bifurcation in three cases: a healthy bifurcation, a bifurcation with a mild stenosis, and the another with a severe stenosis. The result is non-intuitive: there is less chaos for the mild stenosis case even when compared to the healthy, non-stenosed, bifurcation. This happens because the partial obstruction of the mild stenosis generates a symmetry in the flow that does not exist for the healthy condition. For the severe stenosis, there is more irregular motion and more particle trapping as expected.

Ecology and Evolution in the RNA World Dynamics and Stability of Prebiotic Replicator Systems

As of today, the most credible scientific paradigm pertaining to the origin of life on Earth is undoubtedly the RNA World scenario. It is built on the assumption that catalytically active replicators (most probably RNA-like macromolecules) may have been responsible for booting up life almost four billion years ago. The many different incarnations of nucleotide sequence (string) replicator models proposed recently are all attempts to explain on this basis how the genetic information transfer and the functional diversity of prebiotic replicator systems may have emerged, persisted and evolved into the first living cell. We have postulated three necessary conditions for an RNA World model system to be a dynamically feasible representation of prebiotic chemical evolution: (1) it must maintain and transfer a sufficient diversity of information reliably and indefinitely, (2) it must be ecologically stable and (3) it must be evolutionarily stable. In this review, we discuss the best-known prebiotic scenarios and the corresponding models of string-replicator dynamics and assess them against these criteria. We suggest that the most popular of prebiotic replicator systems, the hypercycle, is probably the worst performer in almost all of these respects, whereas a few other model concepts (parabolic replicator, open chaotic flows, stochastic corrector, metabolically coupled replicator system) are promising candidates for development into coherent models that may become experimentally accessible in the future.

Direct experimental visualization of the global Hamiltonian progression of two-dimensional Lagrangian flow topologies from integrable to chaotic state

Countless theoretical/numerical studies on transport and mixing in two-dimensional (2D) unsteady flows lean on the assumption that Hamiltonian mechanisms govern the Lagrangian dynamics of passive tracers. However, experimental studies specifically investigating said mechanisms are rare. Moreover, they typically concern local behavior in specific states (usually far away from the integrable state) and generally expose this indirectly by dye visualization. Laboratory experiments explicitly addressing the global Hamiltonian progression of the Lagrangian flow topology entirely from integrable to chaotic state, i.e., the fundamental route to efficient transport by chaotic advection, appear non-existent. This motivates our study on experimental visualization of this progression by direct measurement of Poincaré sections of passive tracer particles in a representative 2D time-periodic flow. This admits (i) accurate replication of the experimental initial conditions, facilitating true one-to-one comparison of simulated and measured behavior, and (ii) direct experimental investigation of the ensuing Lagrangian dynamics. The analysis reveals a close agreement between computations and observations and thus experimentally validates the full global Hamiltonian progression at a great level of detail.

Recurrence-time statistics in non-Hamiltonian volume-preserving maps and flows

We analyze the recurrence-time statistics (RTS) in three-dimensional non-Hamiltonian volume-preserving systems (VPS): an extended standard map and a fluid model. The extended map is a standard map weakly coupled to an extra dimension which contains a deterministic regular, mixed (regular and chaotic), or chaotic motion. The extra dimension strongly enhances the trapping times inducing plateaus and distinct algebraic and exponential decays in the RTS plots. The combined analysis of the RTS with the classification of ordered and chaotic regimes and scaling properties allows us to describe the intricate way trajectories penetrate the previously impenetrable regular islands from the uncoupled case. Essentially the plateaus found in the RTS are related to trajectories that stay for long times inside trapping tubes, not allowing recurrences, and then penetrate diffusively the islands (from the uncoupled case) by a diffusive motion along such tubes in the extra dimension. All asymptotic exponential decays for the RTS are related to an ordered regime (quasiregular motion), and a mixing dynamics is conjectured for the model. These results are compared to the RTS of the standard map with dissipation or noise, showing the peculiarities obtained by using three-dimensional VPS. We also analyze the RTS for a fluid model and show remarkable similarities to the RTS in the extended standard map problem.

Noise-enhanced trapping in chaotic scattering

We show that noise enhances the trapping of trajectories in scattering systems. In fully chaotic systems, the decay rate can decrease with increasing noise due to a generic mismatch between the noiseless escape rate and the value predicted by the Liouville measure of the exit set. In Hamiltonian systems with mixed phase space we show that noise leads to a slower algebraic decay due to trajectories performing a random walk inside Kolmogorov-Arnold-Moser islands. We argue that these noise-enhanced trapping mechanisms exist in most scattering systems and are likely to be dominant for small noise intensities, which is confirmed through a detailed investigation in the Hénon map. Our results can be tested in fluid experiments, affect the fractal Weyl's law of quantum systems, and modify the estimations of chemical reaction rates based on phase-space transition state theory.

Slow decay of concentration variance due to no-slip walls in chaotic mixing

Chaotic mixing in a closed vessel is studied experimentally and numerically in different two-dimensional (2D) flow configurations. For a purely hyperbolic phase space, it is well known that concentration fluctuations converge to an eigenmode of the advection-diffusion operator and decay exponentially with time. We illustrate how the unstable manifold of hyperbolic periodic points dominates the resulting persistent pattern. We show for different physical viscous flows that, in the case of a fully chaotic Poincaré section, parabolic periodic points at the walls lead to slower (algebraic) decay. A persistent pattern, the backbone of which is the unstable manifold of parabolic points, can be observed. However, slow stretching at the wall forbids the rapid propagation of stretched filaments throughout the whole domain, and hence delays the formation of an eigenmode until it is no longer experimentally observable. Inspired by the baker's map, we introduce a 1D model with a parabolic point that gives a good account of the slow decay observed in experiments. We derive a universal decay law for such systems parametrized by the rate at which a particle approaches the no-slip wall.

Effective dimensions and chemical reactions in fluid flows

We show that chemical activity in hydrodynamical flows can be understood as the outcome of three basic effects: the stirring protocol of the flow, the local properties of the reaction, and the global folding dynamics which also depends on the geometry of the container. The essence of each of these components can be described by simple functional relations. In an ordinary differential equation approach, they determine a new chemical rate equation for the concentration, which turns out to be coupled to the dynamics of an effective fractal dimension. The theory predicts an exponential convergence to the asymptotic chemical state. This holds even in flows characterized by a linear stirring protocol where transient fractal patterns are shown to exist despite the lack of any chaotic set of the advection dynamics. In the exponential case the theory applies to flows of chaotic time dependence (chaotic flows) as well.

Competitive exclusion and limiting similarity: A unified theory

Robustness of coexistence against changes of parameters is investigated in a model-independent manner by analyzing the feedback loop of population regulation. We define coexistence as a fixed point of the community dynamics with no population having zero size. It is demonstrated that the parameter range allowing coexistence shrinks and disappears when the Jacobian of the dynamics decreases to zero. A general notion of regulating factors/variables is introduced. For each population, its impact and sensitivity niches are defined as the differential impact on, and the differential sensitivity towards, the regulating variables, respectively. Either the similarity of the impact niches or the similarity of the sensitivity niches results in a small Jacobian and in a reduced likelihood of coexistence. For the case of a resource continuum, this result reduces to the usual "limited niche overlap" picture for both kinds of niche. As an extension of these ideas to the coexistence of infinitely many species, we demonstrate that Roughgarden's example for coexistence of a continuum of populations is structurally unstable.

Chemical transients in closed chaotic flows: the role of effective dimensions

We investigate chemical activity in hydrodynamical flows in closed containers. In contrast to open flows, in closed flows the chemical field does not show a well-defined fractal property; nevertheless, there is a transient filamentary structure present. We show that the effect of the filamentary patterns on the chemical activity can be modeled by the use of time-dependent effective dimensions. We derive a new chemical rate equation, which turns out to be coupled to the dynamics of the effective dimension, and predicts an exponential convergence. Previous results concerning activity in open flows are special cases of this new rate equation.

Fractal scaling of microbial colonies affects growth

The growth dynamics of filamentary microbial colonies is investigated. Fractality of the fungal or actinomycetes colonies is shown both theoretically and in numerical experiments to play an important role. The growth observed in real colonies is described by the assumption of time-dependent fractality related to the different ages of various parts of the colony. The theoretical results are compared to a simulation based on branching random walks.

Multifractal spectra of chemical fields in fluid flows

In the filamental phase of reactions embedded in fluid flows, where the concentration distribution is strongly fluctuating, we show that a chemical measure can be defined based on the absolute value of the concentration gradients. We express the generalized dimensions in terms of the roughness exponents of the structure functions as well as of the cancellation exponents of the chemical concentration. This measure is of basically different character than the natural distribution of the passive advection. It is similar to the SRB measures of dissipative systems, although the advection problem is area preserving. This approach is shown to be a useful tool in analyzing sea surface temperature anomalies.

Advection diffusion in nonchaotic closed flows: non-Hermitian operators, universality, and localization

The qualitative spectral properties characterizing the advection-diffusion operator in two-dimensional steady incompressible flows can be obtained from the analysis of simple model flows on the torus, the velocity field of which attains the simple expression v (x) = (0, v(y) (x) ) . For this class of simple flows, the advection-diffusion operator reduces to a one-dimensional Schrödinger operator in the presence of an imaginary potential, which shares some spectral analogies with non-Hermitian quantum operators (e.g., spectral invariance), and is characterized by eigenfunction localization. The latter property (i.e., eigenfunction localization) is strictly related to the occurrence of a universal scaling of the eigenvalue spectrum with the Peclet number, the scaling exponent of which depends exclusively on the local behavior of the potential close to its critical points. The analysis is extended to a class of unbounded non-Hermitian operators, which include the Laplacian and the biharmonic operators coupled to an imaginary potential as special cases.

Reactions in flows with nonhyperbolic dynamics

We study the reaction dynamics of active particles that are advected passively by 2D incompressible open flows, whose motion is nonhyperbolic. This nonhyperbolicity is associated with the presence of persistent vortices near the wake, wherein fluid is trapped. We show that the fractal equilibrium distribution of the reactants is described by an effective dimension d(eff) , which is a finite resolution approximation to the fractal dimension. Furthermore, d(eff) depends on the resolution epsilon and on the reaction rate 1/tau . As tau is increased, the equilibrium distribution goes through a series of transitions where the effective dimension increases abruptly. These transitions are determined by the complex structure of Cantori surrounding the Kolmogorov-Arnold-Moser (KAM) islands.

Spatial models of prebiotic evolution: soup before pizza?

The problem of information integration and resistance to the invasion of parasitic mutants in prebiotic replicator systems is a notorious issue of research on the origin of life. Almost all theoretical studies published so far have demonstrated that some kind of spatial structure is indispensable for the persistence and/or the parasite resistance of any feasible replicator system. Based on a detailed critical survey of spatial models on prebiotic information integration, we suggest a possible scenario for replicator system evolution leading to the emergence of the first protocells capable of independent life. We show that even the spatial versions of the hypercycle model are vulnerable to selfish parasites in heterogeneous habitats. Contrary, the metabolic system remains persistent and coexistent with its parasites both on heterogeneous surfaces and in chaotically mixing flowing media. Persistent metabolic parasites can be converted to metabolic cooperators, or they can gradually obtain replicase activity. Our simulations show that, once replicase activity emerged, a gradual and simultaneous evolutionary improvement of replicase functionality (speed and fidelity) and template efficiency is possible only on a surface that constrains the mobility of macromolecule replicators. Based on the results of the models reviewed, we suggest that open chaotic flows ('soup') and surface dynamics ('pizza') both played key roles in the sequence of evolutionary events ultimately concluding in the appearance of the first living cell on Earth.

Competing populations in flows with chaotic mixing

We investigate the effects of spatial heterogeneity on the coexistence of competing species in the case when the heterogeneity is dynamically generated by environmental flows with chaotic mixing properties. We show that one effect of chaotic advection on the passively advected species (such as phytoplankton, or self-replicating macro-molecules) is the possibility of coexistence of more species than that limited by the number of niches they occupy. We derive a novel set of dynamical equations for competing populations.

Characterization of finite-time Lyapunov exponents and vectors in two-dimensional turbulence

This paper discusses the application of Lyapunov theory in chaotic systems to the dynamics of tracer gradients in two-dimensional flows. The Lyapunov theory indicates that more attention should be given to the Lyapunov vector orientation. Moreover, the properties of Lyapunov vectors and exponents are explained in light of recent results on tracer gradients dynamics. Differences between the different Lyapunov vectors can be interpreted in terms of competition between the effects of effective rotation and strain. Also, the differences between backward and forward vectors give information on the local reversibility of the tracer gradient dynamics. A numerical simulation of two-dimensional turbulence serves to highlight these points and the spatial distribution of finite time Lyapunov exponents is also discussed in relation to stirring properties. (c) 2002 American Institute of Physics.

Autocatalytic reactions of phase distributed active particles

We investigate the effect of asynchronism of autocatalytic reactions taking place in open hydrodynamical flows, by assigning a phase to each particle in the system to differentiate the timing of the reaction, while the reaction rate (periodicity) is kept unchanged. The chaotic saddle in the flow dynamics acts as a catalyst and enhances the reaction in the same fashion as in the case of a synchronous reaction that was studied previously, proving that the same type of nonlinear reaction kinetics is valid in the phase-distributed situation. More importantly, we show that, in a certain range of a parameter, the phenomenon of phase selection can occur, when a group of particles with a particular phase is favored over the others, thus occupying a larger fraction of the available space, or eventually leading to the extinction of the unfavored phases. We discuss the biological relevance of this latter phenomenon. (c) 2002 American Institute of Physics.

Metabolic network dynamics in open chaotic flow

We have analyzed the dynamics of metabolically coupled replicators in open chaotic flows. Replicators contribute to a common metabolism producing energy-rich monomers necessary for replication. The flow and the biological processes take place on a rectangular grid. There can be at most one molecule on each grid cell, and replication can occur only at localities where all the necessary replicators (metabolic enzymes) are present within a certain neighborhood distance. Due to this finite metabolic neighborhood size and imperfect mixing along the fractal filaments produced by the flow, replicators can coexist in this fluid system, even though coexistence is impossible in the mean-field approximation of the model. We have shown numerically that coexistence mainly depends on the metabolic neighborhood size, the kinetic parameters, and the number of replicators coupled through metabolism. Selfish parasite replicators cannot destroy the system of coexisting metabolic replicators, but they frequently remain persistent in the system. (c) 2002 American Institute of Physics.

Finite-size effects on active chaotic advection

A small (but finite-size) spherical particle advected by fluid flows obeys equations of motion that are inherently dissipative, due to the Stokes drag. The dynamics of the advected particle can be chaotic even with a flow field that is simply time periodic. Similar to the case of ideal tracers, whose dynamics is Hamiltonian, chemical or biological activity involving such particles can be analyzed using the theory of chaotic dynamics. Using the example of an autocatalytic reaction, A+Bright arrow2B, we show that the balance between dissipation in the particle dynamics and production due to reaction leads to a steady state distribution of the reagent. We also show that, in the case of coalescence reaction, B+Bright arrowB, the decay of the particle density obeys a universal scaling law as approximately t(minus sign1) and that the particle distribution becomes restricted to a subset with fractal dimension D2, where D2 is the correlation dimension of the chaotic attractor in the particle dynamics.

Geometry of reaction interfaces in chaotic flows

The analysis of transport-controlled reactions in chaotic flows provides a physical frame to extend the concept of the intermaterial contact area (ICA)--introduced in the purely kinematic case--to mixing systems with diffusion, where the ICA is identified through the reaction interface between segregated reactants. We show that the dynamics of the ICA undergoes a crossover from kinematics-dominated exponential growth to a persistent oscillatory regime resulting from the intertwined action of advection and diffusion. The scaling of the crossover length versus the Peclet number is analyzed.

Population dynamics advected by chaotic flows: A discrete-time map approach

A discrete-time model of reacting evolving fields, transported by a bidimensional chaotic fluid flow, is studied. Our approach is based on the use of a Lagrangian scheme where fluid particles are advected by a two-dimensional symplectic map possibly yielding Lagrangian chaos. Each fluid particle carries concentrations of active substances which evolve according to its own reaction dynamics. This evolution is also modeled in terms of maps. Motivated by the question, of relevance in marine ecology, of how a localized distribution of nutrients or preys affects the spatial structure of predators transported by a fluid flow, we study a specific model in which the population dynamics is given by a logistic map with space-dependent coefficient, and advection is given by the standard map. Fractal and random patterns in the Eulerian spatial concentration of predators are obtained under different conditions. Exploiting the analogies of this coupled-map (advection plus reaction) system with a random map, some features of these patterns are discussed. (c) 2001 American Institute of Physics.

Chaotic flow: the physics of species coexistence

Hydrodynamical phenomena play a keystone role in the population dynamics of passively advected species such as phytoplankton and replicating macromolecules. Recent developments in the field of chaotic advection in hydrodynamical flows encourage us to revisit the population dynamics of species competing for the same resource in an open aquatic system. If this aquatic environment is homogeneous and well-mixed then classical studies predict competitive exclusion of all but the most perfectly adapted species. In fact, this homogeneity is very rare, and the species of the community (at least on an ecological observation time scale) are in nonequilibrium coexistence. We argue that a peculiar small-scale, spatial heterogeneity generated by chaotic advection can lead to coexistence. In open flows this imperfect mixing lets the populations accumulate along fractal filaments, where competition is governed by an "advantage of rarity" principle. The possibility of this generic coexistence sheds light on the enrichment of phytoplankton and the information integration in early macromolecule evolution.