Macroscopic transport in mixed phase space Hamiltonian systems and the role of a distinct time-scale for the power-law decay.

Motivated by the losses of runaway electrons during disruptive events in present and future tokamaks like the ITER, we investigate the transport in mixed phase space Hamiltonian systems. We are interested in the regime where the sticky regions, remaining after the disintegration of invariant transport barriers, form layers in the phase space separated by partial barriers to transport. The example we use is the standard map.

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.

Unrevealed part of myosin's powerstroke accounts for high efficiency of muscle contraction.

Background: Myosin II, the motor protein driving muscle contraction, uses energy of ATP hydrolysis to produce movement along actin. The key step of energy transduction is the powerstroke, involving rotation of myosin's lever while myosin is attached to actin. Macroscopic measurements indicated high thermodynamic efficiency for energy conversion.

Emerging fractal patterns in a real 3D cerebral aneurysm.

The behaviour of biological fluid flows is often investigated in medical practice to draw conclusions on the physiological or pathological conditions of the considered organs. One area where such investigations are proven to be useful is the flow-related formation and growth of different pathologic malformations of the cerebro-vascular system. In this work, a detailed study is presented on the effect of a cerebral aneurysm on blood transport inside a human brain artery segment.

Doubly transient chaos: generic form of chaos in autonomous dissipative systems.

Chaos is an inherently dynamical phenomenon traditionally studied for trajectories that are either permanently erratic or transiently influenced by permanently erratic ones lying on a set of measure zero. The latter gives rise to the final state sensitivity observed in connection with fractal basin boundaries in conservative scattering systems and driven dissipative systems. Here we focus on the most prevalent case of undriven dissipative systems, whose transient dynamics fall outside the scope of previous studies since no time-dependent solutions can exist for asymptotically long times.

Driving a conceptual model climate by different processes: snapshot attractors and extreme events.

In a low-order chaotic model of global atmospheric circulation the effects of driving, i.e., time-dependent (periodic, chaotic, and noisy) forcing, are investigated, with particular interest in extremal behavior.

Are the fractal skeletons the explanation for the narrowing of arteries due to cell trapping in a disturbed blood flow?

We show that common circulatory diseases, such as stenoses and aneurysms, generate chaotic advection of blood particles. This phenomenon has major consequences on the way the biochemical particles behave. Chaotic advection leads to a peculiar filamentary particle distribution, which in turn creates a favorable environment for particle reactions.

Fractal snapshot components in chaos induced by strong noise.

In systems exhibiting transient chaos in coexistence with periodic attractors, the inclusion of weak noise might give rise to noise-induced chaotic attractors. When the noise amplitude exceeds a critical value, an extended attractor appears along the fractal unstable manifold of the underlying nonattracting chaotic set. A further increase of noise leads to a fuzzy nonfractal pattern.

Fractal structures in stenoses and aneurysms in blood vessels.

Recent advances in the field of chaotic advection provide the impetus to revisit the dynamics of particles transported by blood flow in the presence of vessel wall irregularities. The irregularity, being either a narrowing or expansion of the vessel, mimicking stenoses or aneurysms, generates abnormal flow patterns that lead to a peculiar filamentary distribution of advected particles, which, in the blood, would include platelets. Using a simple model, we show how the filamentary distribution depends on the size of the vessel wall irregularity, and how it varies under resting or exercise conditions.

Chaotic advection in blood flow.

In this paper we argue that the effects of irregular chaotic motion of particles transported by blood can play a major role in the development of serious circulatory diseases. Vessel wall irregularities modify the flow field, changing in a nontrivial way the transport and activation of biochemically active particles. We argue that blood particle transport is often chaotic in realistic physiological conditions.

Onset of chaotic advection in open flows.

In this paper we investigate the transition to chaos in the motion of particles advected by open flows with obstacles. By means of a topological argument, we show that the separation points on the surface of the obstacle imply the existence of a saddle point downstream from the obstacle, with an associated heteroclinic orbit. We argue that as soon as the flow becomes time periodic, these orbits give rise to heteroclinic tangles, causing passively advected particles to experience transient chaos.

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.

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.

Conservative spatial chaos of buckled elastic linkages.

Buckling of an elastic linkage under general loading is investigated. We show that buckling is related to an initial value problem, which is always a conservative, area-preserving mapping, even if the original static problem is nonconservative. In some special cases, we construct the global bifurcation diagrams, and argue that their complicated structure is a consequence of spatial chaos.

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.

Rock-scissors-paper game in a chaotic flow: the effect of dispersion on the cyclic competition of microorganisms.

Laboratory experiments and numerical simulations have shown that the outcome of cyclic competition is significantly affected by the spatial distribution of the competitors. Short-range interaction and limited dispersion allows for coexistence of competing species that cannot coexist in a well-mixed environment. In order to elucidate the mechanisms that destroy species diversity we study the intermediate situation of imperfect mixing, typical in aquatic media, in a model of cyclic competition between toxin producing, sensitive and resistant phenotypes.

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.

Growth induced curve dynamics for filamentary micro-organisms.

The growth of filamentary micro-organisms is described in terms of the geometry of evolving planar curves in which the dynamics is determined by an underlying growth process. Steadily propagating tip shapes in two and three dimensions are found that are consistent with experimentally observed growth sequences.

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.

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.

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.

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.

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.

Chemical or biological activity in open chaotic flows.

We investigate the evolution of particle ensembles in open chaotic hydrodynamical flows. Active processes of the type A+B-->2B and A+B-->2C are considered in the limit of weak diffusion. As an illustrative advection dynamics we consider a model of the von Kármán vortex street, a time-periodic two-dimensional flow of a viscous fluid around a cylinder.

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.