Chemical or biological activity in open chaotic flows

Fractals and Chaos in the Hemodynamics of Intracranial Aneurysms

Computing the emerging flow in blood vessel sections by means of computational fluid dynamics is an often applied practice in hemodynamics research. One particular area for such investigations is related to the cerebral aneurysms, since their formation, pathogenesis, and the risk of a potential rupture may be flow-related. We present a study on the behavior of small advected particles in cerebral vessel sections in the presence of aneurysmal malformations. These malformations cause strong flow disturbances driving the system toward chaotic behavior. Within these flows, the particle trajectories can form a fractal structure, the properties of which are measurable by quantitative techniques. The measurable quantities are well established chaotic properties, such as the Lyapunov exponent, escape rate, and information dimension. Based on these findings, we propose that chaotic flow within blood vessels in the vicinity of the aneurysm might be relevant for the pathogenesis and development of this malformation.

Competitive autocatalytic reactions in chaotic flows with diffusion: prediction using finite-time Lyapunov exponents

We investigate chaotic advection and diffusion in autocatalytic reactions for time-periodic sine flow computationally using a mapping method with operator splitting. We specifically consider three different autocatalytic reaction schemes: a single autocatalytic reaction, competitive autocatalytic reactions, which can provide insight into problems of chiral symmetry breaking and homochirality, and competitive autocatalytic reactions with recycling. In competitive autocatalytic reactions, species B and C both undergo an autocatalytic reaction with species A such that [Formula: see text] and [Formula: see text]. Small amounts of initially spatially localized B and C and a large amount of spatially homogeneous A are advected by the velocity field, diffuse, and react until A is completely consumed and only B and C remain. We find that local finite-time Lyapunov exponents (FTLEs) can accurately predict the final average concentrations of B and C after the reaction completes. The species that starts in the region with the larger FTLE has, with high probability, the larger average concentration at the end of the reaction. If B and C start in regions with similar FTLEs, their average concentrations at the end of the reaction will also be similar. When a recycling reaction is added, the system evolves towards a single species state, with the FTLE often being useful in predicting which species fills the entire domain and which is depleted. The FTLE approach is also demonstrated for competitive autocatalytic reactions in journal bearing flow, an experimentally realizable flow that generates chaotic dynamics.

The role of structured stirring and mixing on gamete dispersal and aggregation in broadcast spawning

Broadcast-spawning benthic invertebrates synchronously release sperm and eggs from separate locations into the surrounding flow, whereupon the process depends on structured stirring by the flow field (at large scales), and sperm motility and taxis (at small scales) to bring the gametes together. The details of the relevant physical and biological aspects of the problem that result in successful and efficient fertilization are not well understood. This review paper includes relevant work from both the physical and biological communities to synthesize a more complete understanding of the processes that govern fertilization success; the focus is on the role of structured stirring on the dispersal and aggregation of gametes. The review also includes a summary of current trends and approaches for numerical and experimental simulations of broadcast spawning.

Reacting particles in open chaotic flows

We study the collision probability p of particles advected by open flows with chaotic advection. We show that p scales with the particle size (or, alternatively, reaction distance) δ as a power law whose coefficient is determined by the fractal dimensions of the invariant sets defined by the advection dynamics. We also argue that this same scaling also holds for the reaction rate of active particles in the low-density regime. These analytical results are compared to numerical simulations, and they are found to agree very well.

Coexistence of inertial competitors in chaotic flows

We investigate the dynamics of inertial particles immersed in open chaotic flows. We consider the generic problem of competition between different species, e.g., phytoplankton populations in oceans. The strong influence from inertial effects is shown to result in the persistence of different species even in cases when the passively advected species cannot coexist. Multispecies coexistence in the ocean can be explained by the fact that the unstable manifold is different for each advected competitor of different size.

Synchronization of oscillating reactions in an extended fluid system

We present experiments on the synchronization of a dynamical, chemical process in an extended, flowing, fluid system. The oscillatory Belousov-Zhabotinsky chemical reaction is the process studied, and the flow is an annular chain of counterrotating vortices. Azimuthal motion of the vortices is controlled externally, enabling us to vary the type of transport. We find that oscillations of the Belousov-Zhabotinsky reaction synchronize throughout the extended fluid system only if transport in the flow is superdiffusive, with tracers in the flow undergoing rapid, distant jumps called Lévy flights.

Finite-size effects on open chaotic advection

We study the effects of finite-sizeness on small, neutrally buoyant, spherical particles advected by open chaotic flows. We show that, when observed in the configuration or physical space, the advected finite-size particles disperse about the unstable manifold of the chaotic saddle that governs the passive advection. Using a discrete-time system for the dynamics, we obtain an expression predicting the dispersion of the finite-size particles in terms of their Stokes parameter at the onset of the finite-size induced dispersion. We test our theory in a system derived from a flow and find remarkable agreement between our expression and the numerically measured dispersion.

Discrete time model for chemical or biological decay in chaotic flows: reentrance phase transitions

We consider a discrete time model of advection, reaction, and diffusion on a lattice to investigate the steady-state spatial structure of chemically decaying substances. The time discretization of the dynamics has a considerable impact on these structures. Additional smooth-filamental phase transitions, nonexistent in the continuous-time description, appear. We show how these structures and their scaling properties depend on the time step of the discrete dynamics. Exploiting the analogies of this discrete model with the logistic map, some general features are discussed.

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.

Experimental studies of pattern formation in a reaction-advection-diffusion system

Experiments are presented on pattern formation in the Belousov-Zhabotinsky (BZ) reaction in a blinking vortex flow. Mixing in this flow is chaotic, with nearby tracers separating exponentially with time. The patterns that form in this flow with the BZ reaction mimic chaotic mixing structures seen in passive transport. The behavior is analyzed in terms of a mixing time taum and a characteristic decorrelation time TBZ for the BZ system. Flows with taum comparable to or smaller than TBZ generate large-scale patterns whose features are captured by simulations of mixing fields for the flow.

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.

Chemical and biological activity in three-dimensional flows

We study the dynamics of active particles advected by three-dimensional (3D) open incompressible flows, both analytically and numerically. We find that 3D reactive flows have fundamentally different dynamical features from those in 2D systems. In particular, we show that the reaction's productivity per reaction step can be enhanced, with respect to the 2D case, while the productivity per unit time in some 3D flows goes to zero in the limit of high mixing rates, in contrast to the 2D behavior, in which the productivity goes to a finite constant. These theoretical predictions are validated by numerical simulations on a generic map model.

Reactive particles in random flows

We study the dynamics of chemically or biologically active particles advected by open flows of chaotic time dependence, which can be modeled by a random time dependence of the parameters on a stroboscopic map. We develop a general theory for reactions in such random flows, and derive the reaction equation for this case. We show that there is a singular enhancement of the reaction in random flows, and this enhancement is increased as compared to the nonrandom case. We verify our theory in a model flow generated by four point vortices moving chaotically.

Universality in active chaos

Many examples of chemical and biological processes take place in large-scale environmental flows. Such flows generate filamental patterns which are often fractal due to the presence of chaos in the underlying advection dynamics. In such processes, hydrodynamical stirring strongly couples into the reactivity of the advected species and might thus make the traditional treatment of the problem through partial differential equations difficult. Here we present a simple approach for the activity in inhomogeneously stirred flows. We show that the fractal patterns serving as skeletons and catalysts lead to a rate equation with a universal form that is independent of the flow, of the particle properties, and of the details of the active process. One aspect of the universality of our approach is that it also applies to reactions among particles of finite size (so-called inertial particles).

Noise-sustained coherent oscillation of excitable media in a chaotic flow

Constructive effects of noise in spatially extended systems have been well studied in static reaction-diffusion media. We study a noisy two-dimensional Fitz Hugh-Nagumo excitable model under the stirring of a chaotic flow. We find a regime where a noisy excitation can induce a coherent global excitation of the medium and a noise-sustained oscillation. Outside this regime, noisy excitation is either diluted into homogeneous background by strong stirring or develops into noncoherent patterns at weak stirring. These results explain some experimental findings of stirring effects in chemical reactions and are relevant for understanding the effects of natural variability in oceanic plankton bloom.

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.

Spatial structure of passive particles with inertia transported by a chaotic flow

We study the spatial patterns formed by inertial particles suspended on the surface of a smooth chaotic flow. In addition to the well-known phenomenon of clustering, we show that, in the presence of diffusion and when a steady space-dependent source of particles is considered, the density of particles may show smooth or fractal features in the low density areas. The conditions needed for the appearance of these structures and their characterization with the first order structure function are also calculated.

Chaotic mixing induced transitions in reaction-diffusion systems

We study the evolution of a localized perturbation in a chemical system with multiple homogeneous steady states, in the presence of stirring by a fluid flow. Two distinct regimes are found as the rate of stirring is varied relative to the rate of the chemical reaction. When the stirring is fast localized perturbations decay towards a spatially homogeneous state. When the stirring is slow (or fast reaction) localized perturbations propagate by advection in form of a filament with a roughly constant width and exponentially increasing length. The width of the filament depends on the stirring rate and reaction rate but is independent of the initial perturbation. We investigate this problem numerically in both closed and open flow systems and explain the results using a one-dimensional "mean-strain" model for the transverse profile of the filament that captures the interplay between the propagation of the reaction-diffusion front and the stretching due to chaotic advection. (c) 2002 American Institute of Physics.

Small-scale structure of nonlinearly interacting species advected by chaotic flows

We study the spatial patterns formed by interacting biological populations or reacting chemicals under the influence of chaotic flows. Multiple species and nonlinear interactions are explicitly considered, as well as cases of smooth and nonsmooth forcing sources. The small-scale structure can be obtained in terms of characteristic Lyapunov exponents of the flow and of the chemical dynamics. Different kinds of morphological transitions are identified. Numerical results from a three-component plankton dynamics model support the theory, and they serve also to illustrate the influence of asymmetric couplings. (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.

Noise-induced enhancement of chemical reactions in nonlinear flows

Motivated by the problem of ozone production in atmospheres of urban areas, we consider chemical reactions of the general type: A+B-->2C, in idealized two-dimensional nonlinear flows that can generate Lagrangian chaos. Our aims differ from those in the existing work in that we address the role of transient chaos versus sustained chaos and, more importantly, we investigate the influence of noise. We find that noise can significantly enhance the chemical reaction in a resonancelike manner where the product of the reaction becomes maximum at some optimal noise level. We also argue that chaos may not be a necessary condition for the observed resonances. A physical theory is formulated to understand the resonant behavior. (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.

Advective coalescence in chaotic flows

We investigate the reaction kinetics of small spherical particles with inertia, obeying coalescence type of reaction, B+B-->B, and being advected by hydrodynamical flows with time-periodic forcing. In contrast to passive tracers, the particle dynamics is governed by the strongly nonlinear Maxey-Riley equations, which typically create chaos in the spatial component of the particle dynamics, appearing as filamental structures in the distribution of the reactants. Defining a stochastic description supported on the natural measure of the attractor, we show that, in the limit of slow reaction, the reaction kinetics assumes a universal behavior exhibiting a t(-1) decay in the amount of reagents, which become distributed on a subset of dimension D2, where D2 is the correlation dimension of the chaotic flow.

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.

Multifractal structure of chaotically advected chemical fields

The structure of the concentration field of a decaying substance produced by chemical sources and advected by a smooth incompressible two-dimensional flow is investigated. We focus our attention on the nonuniformities of the Holder exponent of the resulting filamental chemical field. They appear most evidently in the case of open flows where irregularities of the field exhibit strong spatial intermittency as they are restricted to a fractal manifold. Nonuniformities of the Holder exponent of the chemical field in closed flows appears as a consequence of the nonuniform stretching of the fluid elements. We study how this affects the scaling exponents of the structure functions, displaying anomalous scaling, and relate the scaling exponents to the distribution of local Lyapunov exponents of the advection dynamics. Theoretical predictions are compared with numerical experiments.

Chaotic advection, diffusion, and reactions in open flows

We review and generalize recent results on advection of particles in open time-periodic hydrodynamical flows. First, the problem of passive advection is considered, and its fractal and chaotic nature is pointed out. Next, we study the effect of weak molecular diffusion or randomness of the flow. Finally, we investigate the influence of passive advection on chemical or biological activity superimposed on open flows. The nondiffusive approach is shown to carry some features of a weak diffusion, due to the finiteness of the reaction range or reaction velocity. (c) 2000 American Institute of Physics.