We study the transition from coherent to incoherent dynamics in a nonlinear triplet of broadband combs of waves. Expanding the analysis of previous works, we investigate what happens when the band of available modes is much larger than that of the initial narrower combs within which the nonlinear interaction is not subjected to selection rules involving wave momenta. Here selection rules are present and active, and we examine how and when coherence can be defined.

Several authors have shown that dissipative thermal cycle models based on finite-time thermodynamics exhibit loop-shaped curves of power output versus efficiency, such as it occurs with actual dissipative thermal engines. Within the context of first-order irreversible thermodynamics (FOIT), in this work we show that for an energy converter consisting of two coupled fluxes it is also possible to find loop-shaped curves of both power output and the so-called ecological function versus efficiency. In a previous work Stucki [J. W. Stucki, Eur. J. Biochem. 109, 269 (1980)] used a FOIT approach to describe the modes of thermodynamic performance of oxidative phosphorylation involved in adenosine triphosphate (ATP) synthesis within mithochondrias. In that work the author did not use the mentioned loop-shaped curves and he proposed that oxidative phosphorylation operates in a steady state at both minimum entropy production and maximum efficiency simultaneously, by means of a conductance matching condition between extreme states of zero and infinite conductances, respectively. In the present work we show that all Stucki’s results about the oxidative phosphorylation energetics can be obtained without the so-called conductance matching condition. On the other hand, we also show that the minimum entropy production state implies both null power output and efficiency and therefore this state is not fulfilled by the oxidative phosphorylation performance. Our results suggest that actual efficiency values of oxidative phosphorylation performance are better described by a mode of operation consisting of the simultaneous maximization of both the so-called ecological function and the efficiency.

The nonlinear transformation of an external noisy signal by an array of noninteracting elements with internal noise is considered. The array simulates a neuronal system that processes spike trains. It is shown that increasing the number of array elements entails significant extending of the stochastic synchronization region and improvement of the signal-to-noise ratio (SNR). The effects are demonstrated for arrays of triggers, overdamped bistable oscillators, and Fitzhugh-Nagumo systems. The interrelation between SNR improvement and the efficiency of information processing is discussed.

A simple spin system with self-interaction is proposed and studied where the interaction among spins is taken into account within a mean field model. The self-interaction, which turns out to be a kind of activation energy, gives rise to slow relaxation due to disorder introduced to the self-interaction. In a thermodynamic limit $(N\to \infty )$, a phase diagram is obtained and a spin-spin time correlation function (TCF) is calculated exactly to show that relaxation time diverges at low temperature. Dynamical property of a finite system, such as relaxation of the TCF, is studied by numerically solving a master equation.

When scroll rings in the excitable Belousov-Zhabotinsky reaction are subjected to an applied electrical current, a reorientation of the scroll ring is induced which is accompanied by a linear drift towards the cathode. The findings can be explained using a modified theory of local filament dynamics under parameter gradients. Numerical simulations using the Oregonator model with an additional advective term accounting for the applied electric field reproduce the experimental results and provide insights into the deformation of the structure of the filament during the reorientation.

The properties of the resonant Gamow states are studied numerically in the semiclassical limit for the quantum Chirikov standard map with absorption. It is shown that the number of such states is described by the fractal Weyl law, and their Husimi distributions closely follow the strange repeller set formed by classical orbits nonescaping in future times. For large matrices the distribution of escape rates converges to a fixed shape profile characterized by a spectral gap related to the classical escape rate.

We investigate the propagation of highly nonlinear solitary waves in heterogeneous, periodic granular media using experiments, numerical simulations, and theoretical analysis. We examine periodic arrangements of particles in experiments in which stiffer and heavier beads (stainless steel) are alternated with softer and lighter ones (polytetrafluoroethylene beads). We find good agreement between experiments and numerics in a model with Hertzian interactions between adjacent beads, which in turn agrees very well with a theoretical analysis of the model in the long-wavelength regime that we derive for heterogeneous environments and general bead interactions. Our analysis encompasses previously studied examples as special cases and also provides key insights into the influence of the dimer lattice on the properties (width and propagation speed) of the highly nonlinear wave solutions.

Consider a classical two-dimensional scattering problem: a ray is scattered by a potential composed of several tall, repelling, steep mountains of arbitrary shape. We study when the traditional approximation of this nonlinear far-from-integrable problem by the corresponding simpler billiard problem, of scattering by hard-wall obstacles of similar shape, is justified. For one class of chaotic scatterers, named here regular Sinai scatterers, the scattering properties of the smooth system indeed limit to those of the billiards. For another class, the singular Sinai scatterers, these two scattering problems have essential differences: though the invariant set of such singular scatterers is hyperbolic (possibly with singularities), that of the smooth flow may have stable periodic orbits, even when the potential is arbitrarily steep. It follows that the fractal dimension of the scattering function of the smooth flow may be significantly altered by changing the ratio between the steepness parameter and a parameter which measures the billiards’ deviation from a singular scatterer. Thus, even in this singular case, the billiard scattering problem is utilized as a skeleton for studying the properties of the smooth flow. Finally, we see that corners have nontrivial and significant impact on the scattering functions.

Using synchronization between observations and a model with undetermined parameters is a natural way to complete the specification of the model. The quality of the synchronization, a cost function to be minimized, typically is evaluated by a least squares difference between the data time series and the model time series. If the coupling between the data and the model is too strong, this cost function is small for any data and any model and the variation of the cost function with respect to the parameters of interest is too small to permit selection of an optimal value of the parameters. We introduce two methods for balancing the competing desires of a small cost function for the quality of the synchronization and the numerical ability to determine parameters accurately. One method of “balanced” synchronization adds to the synchronization cost function a requirement that the conditional Lyapunov exponent of the model system, conditioned on being driven by the data remain negative but small in magnitude. The other method allows the coupling between the data and the model to vary in time according to the error in synchronization. This method succeeds because the data and the model exhibit generalized synchronization in the region where the parameters of the model are well determined. Examples are explored which have deterministic chaos with and without noise in the data signal.

The interaction of two isotropic turbulent fields of equal integral scale but different kinetic energy generates the simplest kind of inhomogeneous turbulent field. In this paper we present a numerical experiment where two time decaying isotropic fields of kinetic energies $E_1$ and $E_2$ initially match over a narrow region. Within this region the kinetic energy varies as a hyperbolic tangent. The following temporal evolution produces a shearless mixing. The anisotropy and intermittency of velocity and velocity derivative statistics is observed. In particular the asymptotic behavior in time and as a function of the energy ratio $E_1∕E_2\to \infty$ is discussed. This limit corresponds to the maximum observable turbulent energy gradient for a given $E_1$ and is obtained through the limit $E_2\to 0$. A field with $E_1∕E_2\to \infty$ represents a mixing which could be observed near a surface subject to a very small velocity gradient separating two turbulent fields, one of which is nearly quiescent. In this condition the turbulent penetration is maximum and reaches a value equal to 1.2 times the nominal mixing layer width. The experiment shows that the presence of a turbulent energy gradient is sufficient for the appearance of intermittency and that during the mixing process the pressure transport is not negligible with respect to the turbulent velocity transport. These findings may open the way to the hypothesis that the presence of a gradient of turbulent energy is the minimal requirement for Gaussian departure in turbulence.

When an electric field is applied to an electrolyte-saturated polymer gel embedded with charged colloidal particles, the force that must be exerted by the hydrogel on each particle reflects a delicate balance of electrical, hydrodynamic, and elastic stresses. This paper examines the displacement of a single charged spherical inclusion embedded in an uncharged hydrogel. We present numerically exact solutions of coupled electrokinetic transport and elastic-deformation equations, where the gel is treated as an incompressible, elastic Brinkman medium. This model problem demonstrates how the displacement depends on the particle size and charge, the electrolyte ionic strength, and Young’s modulus of the polymer skeleton. The numerics are verified, in part, with an analytical (boundary-layer) theory valid when the Debye length is much smaller than the particle radius. Finally, we identify a close connection between the displacement when a colloid is immobilized in a gel and its velocity (electrophoretic mobility) when dispersed in a Newtonian electrolyte.

The two initial stages of spinodal decomposition of a symmetric binary Lennard-Jones fluid have been simulated by molecular dynamics simulations, using a hydrodynamics-conserving thermostat. By analyzing the growth of the average domain size $R\left(t\right)$ with time, a satisfactory agreement is found with the $R\left(t\right)\propto t^{1/3}$ Lifshitz-Slyozov growth law for the early diffusion-driven stage of domain formation in a quenched homogeneous mixture. In the subsequent stage of viscous-dominated growth, the mean domain size appears to follow the linear growth law predicted by Siggia.

Motivated by recent simulations and by experiments on aggregation of gliding bacteria, we study a model of the collective dynamics of self-propelled hard rods on a substrate in two dimensions. The rods have finite size, interact via excluded volume, and their dynamics is overdamped by the interaction with the substrate. Starting from a microscopic model with nonthermal noise sources, a continuum description of the system is derived. The hydrodynamic equations are then used to characterize the possible steady states of the systems and their stability as a function of the particles packing fraction and the speed of self-propulsion.

RNA polymerase (RNAP) is an enzyme that synthesizes a messenger RNA (mRNA) strand which is complementary to a single-stranded DNA template. From the perspective of physicists, an RNAP is a molecular motor that utilizes chemical energy input to move along the track formed by DNA. In many circumstances, which are described in this paper, a large number of RNAPs move simultaneously along the same track; we refer to such collective movements of the RNAPs as RNAP traffic. Here we develop a theoretical model for RNAP traffic by incorporating the steric interactions between RNAPs as well as the mechanochemical cycle of individual RNAPs during the elongation of the mRNA. By a combination of analytical and numerical techniques, we calculate the rates of mRNA synthesis and the average density profile of the RNAPs on the DNA track. We also introduce, and compute, two different measures of fluctuations in the synthesis of RNA. Analyzing these fluctuations, we show how the level of intrinsic noise in mRNA synthesis depends on the concentrations of the RNAPs as well as on those of some of the reactants and the products of the enzymatic reactions catalyzed by RNAP. We suggest appropriate experimental systems and techniques for testing our theoretical predictions.

In a ferroin-catalyzed Belousov-Zhabotinsky (BZ) reaction-diffusion system with reagent concentration gradients, we observed in the experiment a type of spirals with local waves forming groups. Here, we propose an interpretation of the wave grouping phenomenon. The wave grouping mechanism can be well explained in terms of the cooperation of the excitability gradient and the Doppler effect induced by spiral tip’s meandering. In the simulation based on three-dimensional reaction-diffusion system using Oregonator model, spiral patterns analogous to the experiment observation are well reproduced when the parameter gradient in the $z$ direction is introduced.

The rheology and the structure of a dilute semiflexible biofilament solution, like F-actin, interacting via molecular motors is probed by molecular dynamics simulations. Oscillatory external shear is used to measure the storage and loss moduli as a function of motor activity in a range of frequencies and for low shear rates. The overall effect of the motor activity on the rheological properties is interpreted as an increase of the temperature, with the effective temperature proportional to the density of motors. However, the effect of motors on the structural properties of the solution, such as the orientation correlation function, is opposite: the motors drastically increase the orientation correlation length whereas thermal fluctuations decrease it.

We examine a simple model of proton pumping through the inner membrane of mitochondria in the living cell. We demonstrate that the pumping process can be described using approaches of condensed matter physics. In the framework of this model, we show that the resonant Förster-type energy exchange due to electron-proton Coulomb interaction can provide a unidirectional flow of protons against an electrochemical proton gradient, thereby accomplishing proton pumping. The dependence of this effect on temperature as well as electron and proton voltage buildups are obtained taking into account electrostatic forces and noise in the environment. We find that the proton pump works with maximum efficiency in the range of temperatures and transmembrane electrochemical potentials which correspond to the parameters of living cells.

The dynamics of chaotic billiards is significantly influenced by coexisting regions of regular motion. Here we investigate the prevalence of a different fundamental structure, which is formed by marginally unstable periodic orbits and stands apart from the regular regions. We show that these structures both exist and strongly influence the dynamics of locally perturbed billiards, which include a large class of widely studied systems. We demonstrate the impact of these structures in the quantum regime using microwave experiments in annular billiards.

We study experimentally the vortex streets produced by a flapping foil in a hydrodynamic tunnel, using two-dimensional particle image velocimetry. An analysis in terms of a flapping frequency-amplitude phase space allows the identification of (i) the transition from the well-known Bénard–von Kármán (BvK) wake to the reverse BvK vortex street that characterizes propulsive wakes, and (ii) the symmetry breaking of this reverse BvK pattern giving rise to an asymmetric wake. We also show that the transition from a BvK wake to a reverse BvK wake precedes the actual drag-thrust transition and we discuss the significance of the present results in the analysis of flapping systems in nature.

Nonlinear excitations in two-component Bose-Einstein condensates (BECs) described by two coupled Gross-Pitaevskii equations are investigated analytically and numerically. The beating phenomenon, the higher-harmonic generation, and the mixing of the excited modes are revealed by both variational approximation and numerical method. The strong excitations induced by the parametric resonance are also studied by time-periodic modulation for the intercomponent interaction. The resonance conditions in terms of the modulation frequency and the strength of intercomponent interaction are obtained analytically, which are confirmed by numerical method. Direct numerical simulations show that, when the resonance takes place, periodic phase separation and multisoliton configurations (including soliton trains, soliton pairs, and multidomain walls) can be excited. In particular, we demonstrate a method for formation of multisoliton configurations through parametric resonance in two-component BECs.