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The study of hyperbolic waves involves various notions which help characterise how these structures evolve. One important facet is the notion of genuine nonlinearity, namely the ability for shocks and rarefactions to form instead of contact discontinuities. In the context of the Whitham modulation equations, this paper demonstrate that a loss of genuine nonlinearity leads to the appearance of a dispersive set of dynamics in the form of the modified Korteweg de-Vries equation governing the evolution of the waves instead. Its form is universal in the sense that its coefficients can be written entirely using linear properties of the underlying waves such as the conservation laws and linear dispersion relation. This insight is applied to two systems of physical interest, one an optical model and the other a stratified hydrodynamics experiment, to demonstrate how it can be used to provide insight into how waves in these systems evolve when genuine nonlinearity is lost.

We experimentally investigate the stochastic phase dynamics of planar Josephson junctions (JJs) and superconducting quantum interference devices (SQUIDs) defined in epitaxial InAs/Al heterostructures, and characterized by a large ratio of Josephson energy to charging energy. We observe a crossover from a regime of macroscopic quantum tunneling to one of phase diffusion as a function of temperature, where the transition temperature T∗ is gate-tunable. The switching probability distributions are shown to be consistent with a small shunt capacitance and moderate damping, resulting in a switching current which is a small fraction of the critical current. Phase locking between two JJs leads to a difference in switching current between that of a JJ measured in isolation and that of the same JJ measured in an asymmetric SQUID loop. In the case of the loop, T∗ is also tuned by a magnetic flux., Physical Review Letters, 130 (8), ISSN:0031-9007, ISSN:1079-7114

The third-order response lies at the heart of simulating and interpreting nonlinear spectroscopies ranging from two-dimensional infrared (2D-IR) to 2D electronic (2D-ES), and 2D sum frequency generation (2D-SFG). The extra time and frequency dimensions in these spectroscopic techniques provide access to rich information on the electronic and vibrational states present, the coupling between them, and the resulting rates at which they exchange energy that are obscured in linear spectroscopy, particularly for condensed phase systems that usually contain many overlapping features. While the exact quantum expression for the third-order response is well established, it is incompatible with the methods that are practical for calculating the atomistic dynamics of large condensed phase systems. These methods, which include both classical mechanics and quantum dynamics methods that retain quantum statistical properties while obeying the symmetries of classical dynamics, such as LSC-IVR, centroid molecular dynamics, and Ring Polymer Molecular Dynamics (RPMD), naturally provide short-time approximations to the multi-time symmetrized Kubo transformed correlation function. Here, we show how the third-order response can be formulated in terms of equilibrium symmetrized Kubo transformed correlation functions. We demonstrate the utility and accuracy of our approach by showing how it can be used to obtain the third-order response of a series of model systems using both classical dynamics and RPMD. In particular, we show that this approach captures features such as anharmonically induced vertical splittings and peak shifts while providing a physically transparent framework for understanding multidimensional spectroscopies.

We present a brief discussion of the phase-coherent dynamics of discrete breathers (intrinsic localized modes) in a system of two weakly coupled nonlinear chains and its comparison with periodic tunneling of quantum particles in a double-well potential and with macroscopic quantum tunneling of two weakly linked Bose–Einstein condensates. We consider the dynamics of relative phase of classically-tunneling discrete breathers in two weakly coupled nonlinear chains and show that the dynamics of the relative phase in the π/2 tunneling mode coincides with the experimentally observed dynamics of the relative phase of quantum particles, periodically tunneling in a double-well potential, both for noninteracting and strongly repulsively interacting particles. The observed coincidence demonstrates the correspondence between the dynamics of classical localized excitations in two weakly coupled nonlinear chains and tunneling dynamics of quantum object in the double-well potential. We show that in both π/2 and winding tunneling modes the relative phase experiences periodic jumps by π in the instants of complete depopulation of one of the weakly coupled chains or potential wells. The connection of the observed phase dynamics with the non-quantum uncertainty principle is discussed.

We consider networks of coupled phase oscillators of different complexity: Kuramoto–Daido-type networks, generalized Winfree networks, and hypernetworks with triple interactions. For these setups an inverse problem of reconstruction of the network connections and of the coupling function from the observations of the phase dynamics is addressed. We show how a reconstruction based on the minimization of the squared error can be implemented in all these cases. Examples include random networks with full disorder both in the connections and in the coupling functions, as well as networks where the coupling functions are taken from experimental data of electrochemical oscillators. The method can be directly applied to asynchronous dynamics of units, while in the case of synchrony, additional phase resettings are necessary for reconstruction.

International audience; Protonated intermediates are postulated to be involved in the rate determining step of many sugar reactions. This paper presents a study of protonated sugar species, isolated in the gas phase, using a combination of infrared multiple photon dissociation (IRMPD) spectroscopy, classical ab initio molecular dynamics (AIMD) and quantum mechanical vibrational self-consistent field (VSCF) calculations. It provides a likely identification of the reactive intermediate oxocarbenium ion structure in a D-galactosyl system as well as the saccharide pyrolysis product anhydrogalactose (that suggests oxocarbenium ion stabilization), along with the spectrum of the protonated parent species: methyl D-galactopyranoside-H +. Its vibrational fingerprint indicates intramolecular proton sharing. Classical AIMD simulations for galactosyl oxocarbenium ions, conducted in the temperature range ~300-350 K (using B3LYP potentials on-the-fly) reveal efficient transitions on the picosecond timescale. Multiple conformers are likely to exist under the experimental conditions and along with static VSCF calculations, they have facilitated the identification of the individual structural motifs of the galactosyl oxocarbenium ion and protonated anhydrogalactose ion conformers that contribute to the observed experimental spectra. These results demonstrate the power of experimental IRMPD spectroscopy combined with dynamics simulations and with computational spectroscopy at the anharmonic level to unravel conformer structures of protonated saccharides, and to provide information on their lifetimes.

Partial synchronous states appear between full synchrony and asynchrony and exhibit many interesting properties. Most frequently, these states are studied within the framework of phase approximation. The latter is used ubiquitously to analyze coupled oscillatory systems. Typically, the phase dynamics description is obtained in the weak coupling limit, i.e., in the first-order in the coupling strength. The extension beyond the first-order represents an unsolved problem and is an active area of research. In this paper, three partially synchronous states are investigated and presented in order of increasing complexity. First, the usage of the phase response curve for the description of macroscopic oscillators is analyzed. To achieve this, the response of the mean-field oscillations in a model of all-to-all coupled limit-cycle oscillators to pulse stimulation is measured. The next part treats a two-group Kuramoto model, where the interaction of one attractive and one repulsive group results in an interesting solitary state, situated between full synchrony and self-consistent partial synchrony. In the last part, the phase dynamics of a relatively simple system of three Stuart-Landau oscillators are extended beyond the weak coupling limit. The resulting model contains triplet terms in the high-order phase approximation, though the structural connections are only pairwise. Finally, the scaling of the new terms with the coupling is analyzed., Comment: 16 pages, 6 figures

The melting of an ultrathin lubricant film is studied at friction between atomically flat surfaces. We take into account fluctuations of lubricant temperature, which are defined by the Ornstein-Uhlenbeck process. Phase diagrams and portraits are calculated for second- and first-order transitions (the melting of an amorphous and that of a crystalline lubricants, respectively). It is shown that, in the former case, a stick-slip friction domain, separating the regions of dry and sliding friction, appears. In the latter case, three domains of stick-slip friction arise, which are characterized by the transitions between dry, metastable and stable sliding friction. The increase in the correlation time of lubricant temperature fluctuations leads to increasing in the rubbing-surface temperature needed for realization of sliding friction. The stationary states, corresponding to dry, stable and metastable sliding friction, are reached as a result of damped oscillations.

A time dependent thermal model for a superconducting constriction based weak-link (WL) is discussed for investigating the deterministic dynamics of its temperature and phase. A new dynamic regime is found where a non-zero voltage exists across the WL and its temperature stabilizes between the bath temperature and superconductor's critical temperature. This regime exists over a limited bias current range and gives rise to a new hysteretic regime in current-voltage characteristics. We also discuss the effect of fluctuations on the current-voltage characteristics and experimental implications of this dynamic regime., Comment: 7 pages, 4 figures; revised on 25 Nov 2014

Collisions lead to the collapse and revival of the interference fringes between two atomic Bose–Einstein condensates. We study the collapses and revivals of the relative phase between the condensates for two different initial states. One state invokes Bose–broken symmetry allowing us to write the wavefunction as a superposition of total number (of both condensates) states whereas the other does not.

We generalize our recent approach to reconstruction of phase dynamics of coupled oscillators from data [B. Kralemann et al., Phys. Rev. E, 77, 066205 (2008)] to cover the case of small networks of coupled periodic units. Starting from the multivariate time series, we first reconstruct genuine phases and then obtain the coupling functions in terms of these phases. The partial norms of these coupling functions quantify directed coupling between oscillators. We illustrate the method by different network motifs for three coupled oscillators and for random networks of five and nine units. We also discuss nonlinear effects in coupling., Comment: 6 pages, 5 figures, 27 references

We propose a natural two-speed model for the phase dynamics of Si(111) 7x7 phase transition to high-temperature unreconstructed phase. We formulate the phase dynamics by using phase-field method and adaptive mesh refinement. Our simulated results show that a 7x7 island decays with its shape kept unchanged, and its area decay rate is shown to be a constant increasing with its initial area. Low-energy electron microscopy experiments concerned are explained, which confirms that the dimer chains and corner holes are broken first in the transition, and then the stacking fault is remedied slowly. This phase-field method is a reliable approach to phase dynamics of surface phase transitions.

Based on the complex Ginzburg-Landau equation (CGLE), a new mapping model of oscillatory media is proposed. The present dynamics is fully determined by an effective phase field renormalized by amplitude. The model exhibits phase turbulence, amplitude turbulence, and a frozen state reported in the CGLE. In addition, we find a state in which the phase and amplitude have spiral structures with opposite rotational directions. This state is found to be observed also in the CGLE. Thus, one concludes that the behaviors observed in the CGLE can be described by only the phase dynamics appropriately constructed.

We investigate the dynamical properties of two mutually delay-coupled semiconductor lasers that are coupled via their optical fields. Because a semiconductor laser is an oscillator that features strong coupling between its amplitude and phase, this system serves as a prototype model of coupled amplitude-phase oscillators. Our main interest here is in the dynamics near and within the locking region where the two lasers emit light of the same frequency. We present experimental observations that give evidence for four qualitatively different dynamical regimes: stable continuous wave emission, oscillations at the laser's characteristic relaxation oscillation frequency, oscillation related to the frequency difference between the two lasers and more complicated dynamics. We characterize and identify these dynamical regimes and analyse them by means of a bifurcation analysis of the corresponding rate equation model with delay. Specifically, we present the underlying bifurcation structure, where the detuning and the pump current are the main bifurcation parameters. The combination of experiment and bifurcation analysis shows how changes in the dynamics arise from the presence of local and global bifurcations near the locking region. © 2009 IOP Publishing Ltd and London Mathematical Society.

The Kadomstev–Petviashvili (KP) equation is a well-known modulation equation normally derived by starting with the trivial state and an appropriate dispersion relation. In this paper, it is shown that the KP equation is also the relevant modulation equation for bifurcation from periodic travelling waves when the wave action flux has a critical point. Moreover, the emergent KP equation arises in a universal form, with the coefficients determined by the components of the conservation of wave action. The theory is derived for a general class of partial differential equations generated by a Lagrangian using phase modulation. The theory extends to any space dimension and time, but the emphasis in the paper is on the case of 3+1. Motivated by light bullets and quantum vortex dynamics, the theory is illustrated by showing how defocusing NLS in 3+1 bifurcates to KP in 3+1 at criticality. The generalization to N >3 is also discussed.

We derive a new nonlinear criterion for the occurrence of fast relaxation (crash) events at the edge of high-confinement-mode plasmas. These fast relaxation events called ELMs (edge-localized modes) evolve from ideal magnetohydrodynamics (MHD) instabilities, but the crash is not due only to linear physics. We show that for an ELM crash to occur, the coherence time of the relative phase between potential and pressure perturbations must be long enough to allow growth to large amplitude. This phase coherence time is determined by both linear and nonlinear dynamics. An ELM crash requires that the instability growth rate exceed a critical value, i.e., γ>γc, where γc is set by 1/τc and τc is the phase coherence time. For 0

An effective white-noise Langevin equation is derived that describes long-time phase dynamics of a limit-cycle oscillator subjected to weak stationary colored noise. Effective drift and diffusion coefficients are given in terms of the phase sensitivity of the oscillator and the correlation function of the noise, and are explicitly calculated for oscillators with sinusoidal phase sensitivity functions driven by two typical colored Gaussian processes. The results are verified by numerical simulations using several types of stochastic or chaotic noise. The drift and diffusion coefficients of oscillators driven by chaotic noise exhibit anomalous dependence on the oscillator frequency, reflecting the peculiar power spectrum of the chaotic noise., Comment: 16 pages, 6 figures

Recently there has been a surge of new interest in three-dimensional wake patterns. In the present work, we have devised a method to control the spanwise end conditions and wake patterns using “end suction”, which is both continuously-variable and admits transient control. Classical steady-state patterns, such as parallel or oblique shedding or the “chevron” patterns are simply induced. The wake, at a given Reynolds number, is receptive to a continuous range of oblique shedding angles (θ), rather than to discrete angles, and there is excellent agreement with the “cos θ” formula for oblique-shedding frequencies. We show that the laminar shedding regime exists up to Reynolds numbers (Re) of 205, and that the immense disparity among reported critical Re for wake transition (Re = 140–190) can be explained in terms of spanwise end contamination. Our transient experiments have resulted in the discovery of new phenomena such as “phase shocks” and “phase expansions”, which can be explained in terms of a simple model assuming constant normal wavelength of the wake pattern. Peter Monkewitz (Lausanne) also predicts such transient phenomena from a Guinzburg-Landau model for the wake.

We have studied both theoretically and experimentally how an LC series circuit connected in parallel to a Josephson junction influences the Josephson dynamics. The presence of the shell circuit introduces two energy scales, which in specific cases, can strongly differ from the plasma frequency of the isolated junction. Josephson junctions were manufactured using the Nb/Al-AlOx/Nb fabrication technology with various on-chip LC shunt circuits. Spectroscopic measurements in the quantum limit show excellent agreement with theory taking into account the shunt inductance and capacitance in the resistively and capacitively shunted junction model. The results clearly show that the dynamics of the system are two-dimensional, resulting in two resonant modes of the system. These findings have important implications for the design and operation of Josephson junction based quantum bits. (C) 2011 American Institute of Physics. [doi: 10.1063/1.3581139]

We study the collective dynamics of a driven two mode Bose-Hubbard model in the Josephson interaction regime. The classical phase-space is mixed, with chaotic and regular components, that determine the dynamical nature of the fringe-visibility. For weak off-resonant drive, where the chaotic component is small, the many-body dynamics corresponds to that of a Kapitza pendulum, with the relative-phase $\varphi$ between the condensates playing the role of the pendulum angle. Using a master equation approach we show that the modulation of the inter-site potential barrier stabilizes the $\varphi=\pi$ 'inverted pendulum' coherent state, and protects the fringe visibility., Comment: 5 pages, 4 figures

We report a systematic study of the transport properties of high critical temperature superconductor (HTS) biepitaxial Josephson junctions in the submicron range. Junction performances point to more uniform and reproducible devices and to better control of d-wave intrinsic properties. Outcomes promote novel insights into the transport mechanisms across grain boundaries and encourage further developments in the control of dissipation in HTS devices. The application of nanotechnology to HTS could be an additional tool to properly engineer the junction properties to match specific circuit design also in view of the integration into hybrid quantum circuits. (C) 2010 American Institute of Physics. [doi: 10.1063/1.3388035]

We demonstrate in numerical experiments that estimators of strength and directionality of coupling between oscillators based on modeling of their phase dynamics [D.A. Smirnov and B.P. Bezruchko, Phys. Rev. E 68, 046209 (2003)] are widely applicable. Namely, although the expressions for the estimators and their confidence bands are derived for linear uncoupled oscillators under the influence of independent sources of Gaussian white noise, they turn out to allow reliable characterization of coupling from relatively short time series for different properties of noise, significant phase nonlinearity of the oscillators, and non-vanishing coupling between them. We apply the estimators to analyze a two-channel human intracranial epileptic electroencephalogram (EEG) recording with the purpose of epileptic focus localization., Comment: 22 pages, 7 figures, the paper is to be published in Chaos, 2005, vol.15, issue 2, see http://chaos.aip.org/

Although much empirical evidence has demonstrated that p53 plays a key role in tumor suppression, the dynamics and function of the regulatory network centered on p53 have not yet been fully understood. Here, we develop a Boolean network model to reproduce the two-phase dynamics of the p53 network in response to DNA damage. In particular, we map the fates of cells into two types of Boolean attractors, and we find that the apoptosis attractor does not exist for minor DNA damage, reflecting that the cell is reparable. As the amount of DNA damage increases, the basin of the repair attractor shrinks, accompanied by the rising of the apoptosis attractor and the expansion of its basin, indicating that the cell becomes more irreparable with more DNA damage. For severe DNA damage, the repair attractor vanishes, and the apoptosis attractor dominates the state space, accounting for the exclusive fate of death. Based on the Boolean network model, we explore the significance of links, in terms of the sensitivity of the two-phase dynamics, to perturbing the weights of links and removing them. We find that the links are either critical or ordinary, rather than redundant. This implies that the p53 network is irreducible, but tolerant of small mutations at some ordinary links, and this can be interpreted with evolutionary theory. We further devised practical control schemes for steering the system into the apoptosis attractor in the presence of DNA damage by pinning the state of a single node or perturbing the weight of a single link. Our approach offers insights into understanding and controlling the p53 network, which is of paramount importance for medical treatment and genetic engineering.

Scanning tunneling microscope measurements on single crystals of Bi 2 Sr 2 CaCu 2 O 8 + x materials have shown that the d-wave superconductivity in cuprates has nanoscale inhomogeneities and is still robust in spite of theirpresence. We study the dynamics of Josephson coupling between such granular d-wave superconductors, focusing on the effect of nodal Cooper pairs and disorder. We find that the nodal Cooper pairs give rise to a power-law Josephson coupling which leads to the stabilization of the superconducting phase. Our findings suggest that the d-wave superconductivity in an array of grains is unexpectedly robust against a disordering transition, as observed in the experiments. Furthermore, we predict the existence of a planar Josephson-plasmon mode with characteristic frequency that decreases with temperature.

In many chemical reactions, an activation barrier must be overcome before a chemical transformation can occur. As such, understanding the behaviour of molecules in energetically excited states is critical to understanding the chemical changes that these molecules undergo. Among the most prominent reactions for mankind to understand are chemical changes that occur in our own biological molecules. A notable example is the focus towards understanding the interaction of DNA with ultraviolet radiation and the subsequent chemical changes. However, the interaction of radiation with large biological structures is highly complex, and thus the photochemistry of these systems as a whole is poorly understood. Studying the gas-phase spectroscopy and ultrafast dynamics of the building blocks of these more complex biomolecules offers the tantalizing prospect of providing a scientifically intuitive bottom-up approach, beginning with the study of the subunits of large polymeric biomolecules and monitoring the evolution in photochemistry as the complexity of the molecules is increased. While highly attractive, one of the main challenges of this approach is in transferring large, and in many cases, thermally labile molecules into vacuum. This review discusses the recent advances in cutting-edge experimental methodologies, emerging as excellent candidates for progressing this bottom-up approach.

This paper studies the effects of distributed delay coupling on the dynamics in a system of non-identical coupled Stuart-Landau oscillators. For uniform and gamma delay distribution kernels, conditions for amplitude death are obtained in terms of average frequency, frequency detuning and parameters of the coupling, including coupling strength and phase, as well as the mean time delay and the width of the delay distribution. To gain further insight into the dynamics inside amplitude death regions, eigenvalues of the corresponding characteristic equations are computed numerically. Oscillatory dynamics of the system is also investigated using amplitude and phase representation. Various branches of phase-locked solutions are identified, and their stability is analysed for different types of delay distributions., Comment: 25 pages, 13 figures

The application of the transient grating method to the understanding of gas-phase velocity distributions and collisional effects is presented. Theoretical models are discussed in view of the experimental data obtained from iodine vapor. Applications of the transient grating method to other gas-phase problems are also mentioned.

Giant fractional Shapiro steps have been observed in Josephson junction arrays as resulting from magnetic flux quantization in the two-dimensional array. We demonstrate experimentally the appearance of giant fractional Shapiro steps in anisotropic Josephson junction arrays as unambiguous evidence of a skewed current phase relationship. Introducing anisotropy in the array results in a giant collective high frequency response that reflects the properties of a single junction, as evidenced by the observation of a Fraunhofer like magnetic field dependence of the total critical current of the system. The observed phase dynamics can be perfectly captured within an extended resistively shunted Josephson junction model. These results directly indicate the potential of Josephson junction arrays to explore the current phase relation in a very broad frequency range (down to 50 MHz) and in a wide variety of novel link materials exhibiting non-conventional current phase relationships. Giant fractional Shapiro steps have been observed in Josephson junction arrays as resulting from magnetic flux quantization in the two-dimensional array. Here, the authors demonstrate the observation of giant fractional Shapiro steps in an anisotropic Josephson junction array, as unambiguous evidence of a skewed current phase relationship.

Adaptive dynamical networks appear in various real-word systems. One of the simplest phenomenological models for investigating basic properties of adaptive networks is the system of coupled phase oscillators with adaptive couplings. In this paper, we investigate the dynamics of this system. We extend recent results on the appearance of hierarchical frequency-multi-clusters by investigating the effect of the time-scale separation. We show that the slow adaptation in comparison with the fast phase dynamics is necessary for the emergence of the multi-clusters and their stability. Additionally, we study the role of double antipodal clusters, which appear to be unstable for all considered parameter values. We show that such states can be observed for a relatively long time, i.e., they are metastable. A geometrical explanation for such an effect is based on the emergence of a heteroclinic orbit., 16 pages, 8 figures

We develop a technique for the multivariate data analysis of perturbed self-sustained oscillators. The approach is based on the reconstruction of the phase dynamics model from observations and on a subsequent exploration of this model. For the system, driven by several inputs, we suggest a dynamical disentanglement procedure, allowing us to reconstruct the variability of the system's output that is due to a particular observed input, or, alternatively, to reconstruct the variability which is caused by all the inputs except for the observed one. We focus on the application of the method to the vagal component of the heart rate variability caused by a respiratory influence. We develop an algorithm that extracts purely respiratory-related variability, using a respiratory trace and times of R-peaks in the electrocardiogram. The algorithm can be applied to other systems where the observed bivariate data can be represented as a point process and a slow continuous signal, e.g. for the analysis of neuronal spiking., Comment: 10 pages, 8 figures

Synchronization occurs in many natural and technological systems, from cardiac pacemaker cells to coupled lasers. In the synchronized state, the individual cells or lasers coordinate the timing of their oscillations, but they do not move through space. A complementary form of self-organization occurs among swarming insects, flocking birds, or schooling fish; now the individuals move through space, but without conspicuously altering their internal states. Here we explore systems in which both synchronization and swarming occur together. Specifically, we consider oscillators whose phase dynamics and spatial dynamics are coupled. We call them swarmalators, to highlight their dual character. A case study of a generalized Kuramoto model predicts five collective states as possible long-term modes of organization. These states may be observable in groups of sperm, Japanese tree frogs, colloidal suspensions of magnetic particles, and other biological and physical systems in which self-assembly and synchronization interact., Collective self-organized behavior can be observed in a variety of systems such as colloids and microswimmers. Here O’Keeffe et al. propose a model of oscillators which move in space and tend to synchronize with neighboring oscillators and outline five types of collective self-organized states.

We perform experiments and phase model simulations with a ring network of oscillatory electrochemical reactions to explore the effect of random connections and non-isochronocity of the interactions on the pattern formation. A few additional links facilitate the emergence of the fully synchronized state. With larger non-isochronicity, complex rotating waves or persistent irregular phase dynamics can derail the convergence to global synchronization. The observed long transients of irregular phase dynamics exemplify the possibility of a sudden onset of hyper synchronous behavior without any external stimulus or network reorganization., Comment: 4 pages main text and 4 pages supplemental material

Phase plays a crucial role in many quantum effects including interference. Here we lay the foundations for the study of phase in probabilistic theories more generally. Phase is normally defined in terms of complex numbers that appear when representing quantum states as complex vectors. Here we give an operational definition whereby phase is instead defined in terms of measurement statistics. Our definition is phrased in terms of the operational framework known as generalized probabilistic theories or the convex framework. The definition makes it possible to ask whether other theories in this framework can also have phase. We apply our definition to investigate phase and interference in several example theories: classical probability theory, a version of Spekkens' toy model, quantum theory and box-world. We find that phase is ubiquitous; any non-classical theory can be said to have non-trivial phase dynamics. © IOP Publishing and Deutsche Physikalische Gesellschaft.

Synchronization phenomena in a fluid dynamical analogue of atmospheric circulation is studied experimentally by investigating the dynamics of a pair of thermally coupled, rotating baroclinic annulus systems. The coupling between the systems is in the well-known master-slave configuration in both periodic and chaotic regimes. Synchronization tools such as phase dynamics analysis are used to study the dynamics of the coupled system and demonstrate phase synchronization and imperfect phase synchronization, depending upon the coupling strength and parameter mismatch.

We demonstrate that E×B shear, V_{E×B}^{'}, governs the dynamics of the cross phase of the peeling-ballooning-(PB-)mode-driven heat flux, and so determines the evolution from the edge-localized (ELMy) H mode to the quiescent (Q) H mode. A physics-based scaling of the critical E×B shearing rate (V_{E×B,cr}^{'}) for accessing the QH mode is predicted. The ELMy H mode to the QH-mode evolution is shown to follow from the conversion from a phase locked state to a phase slip state. In the phase locked state, PB modes are pumped continuously, so bursts occur. In the slip state, the PB activity is a coherent oscillation. Stronger E×B shearing implies a higher phase slip frequency. This finding predicts a new state of cross phase dynamics and shows a new way to understand the physics mechanism for ELMy to the QH-mode evolution.

We present a novel approach for recovery of the directional connectivity of a small oscillator network by means of the phase dynamics reconstruction from multivariate time series data. The main idea is to use a triplet analysis instead of the traditional pairwise one. Our technique reveals an effective phase connectivity which is generally not equivalent to a structural one. We demonstrate that by comparing the coupling functions from all possible triplets of oscillators, we are able to achieve in the reconstruction a good separation between existing and non-existing connections, and thus reliably reproduce the network structure.

We consider a $\ensuremath{\varphi}$ Josephson junction, which has a bistable zero-voltage state with the stationary phases $\ensuremath{\psi}=\ifmmode\pm\else\textpm\fi{}\ensuremath{\varphi}$. In the nonzero voltage state the phase ``moves'' viscously along a tilted periodic double-well potential. When the tilting is reduced quasistatically, the phase is retrapped in one of the potential wells. We study the viscous phase dynamics to determine in which well ($\ensuremath{-}\ensuremath{\varphi}$ or $+\ensuremath{\varphi}$) the phase is retrapped for a given damping, when the junction returns from the finite-voltage state back to the zero-voltage state. In the limit of low damping, the $\ensuremath{\varphi}$ Josephson junction exhibits a butterfly effect---extreme sensitivity of the destination well on damping. This leads to an impossibility to predict the destination well.

We study the relationship between synchronization and the rate with which information is exchanged between nodes in a spatio-temporal network that describes the dynamics of classical particles under a substrate Remoissenet-Peyrard potential. We also show how phase and complete synchronization can be detected in this network. The difficulty in detecting phase synchronization in such a network appears due to the highly non-coherent character of the particle dynamics which unables a proper definition of the phase dynamics. The difficulty in detecting complete synchronization appears due to the spatio character of the potential which results in an asymptotic state highly dependent on the initial state., to appear in PRAMANA

We demonstrate that a multiple delayed feedback is a powerful tool to control coherence properties of autonomous self-sustained oscillators. We derive the equation for the phase dynamics in presence of noise and delay, and analyze it analytically. In Gaussian approximation a closed set of equations for the frequency and the diffusion constant is obtained. Solutions of these equations are in good agreement with direct numerical simulations.

We measure the velocities of the mean flows that are driven by curved rolls in a pattern formation system. Curved rolls in Faraday waves are generated in experimental cells consisting of channels with varying widths. The mean flow magnitudes are found to scale linearly with roll curvatures and squares of wave amplitudes, agreeing with the prediction from the analysis of phase dynamics expansion. The effects of the mean flows on reducing roll curvatures are also seen.

Binary fluorescence time series obtained from single-molecule imaging experiments can be used to infer protein binding kinetics, in particular, association and dissociation rate constants from waiting time statistics of fluorescence intensity changes. In many cases, rate constants inferred from fluorescence time series exhibit nonintuitive dependence on ligand concentration. Here we examine several possible mechanistic and technical origins that may induce ligand dependence of rate constants. Using aggregated Markov models, we show under the condition of detailed balance that non-fluorescent bindings and missed events due to transient interactions, instead of conformation fluctuations, may underly the dependence of waiting times and thus apparent rate constants on ligand concentrations. In general, waiting times are rational functions of ligand concentration. The shape of concentration dependence is qualitatively affected by the number of binding sites in the single molecule and is quantitatively tuned by model parameters. We also show that ligand dependence can be caused by non-equilibrium conditions which result in violations of detailed balance and require an energy source. As to a different but significant mechanism, we examine the effect of ambient buffers that can substantially reduce the effective concentration of ligands that interact with the single molecules. To demonstrate the effects by these mechanisms, we applied our results to analyze the concentration dependence in a single-molecule experiment EGFR binding to fluorophore-labeled adaptor protein Grb2 by Morimatsu et al. (PNAS,104:18013,2007)., 11 pages, 4 figures; J. Chem. Phys., 137, 2012

For more than three decades, the classical or mean-field picture describing the distant dipolar field has been almost always simplified to an effective field proportional to the local longitudinal magnetization, differing only by a scale factor of 1.5 for homomolecular (identical resonance frequency) and heteromolecular interactions. We re-examine the underlying assumptions, and show both theoretically and experimentally that the mathematical framework needs to be modified for modern applications such as imaging. We demonstrate new pulse sequences which produce unexpected effects; for example, modulating an arbitrarily small fraction of the magnetization can substantially alter the frequency evolution. Thus, matched gradient pulse pairs (a seemingly innocuous module in thousands of existing pulse sequences) can alter the time evolution in highly unexpected ways, particularly with small flip angle pulses such as those used in hyperpolarized experiments. We also show that specific gradient pulse combinations can retain only dipolar interactions between unlike spins, and the dipolar field can generate a secular Hamiltonian proportional to I(x).

Ultrafast vibrational spectra of the aqueous oxalate ion in the region of its carboxylate asymmetric stretch modes show novel relaxation processes. Two-dimensional infrared vibrational echo spectra and the vibrational dynamics obtained from them along with measurements of the anisotropy decay provide a picture in which the localization of the oxalate vibrational excitation onto the carboxylate groups occurs in ∼450 fs. Molecular dynamics simulations are used to characterize the vibrational dynamics in terms of dihedral angle motion between the two carboxylate planes and solvation dynamics. The localization of the oxalate vibrational excitation onto the carboxylates is induced by the fluctuations in the carboxylate vibrational frequencies which are shown by theory and experiment to have a similar correlation time as the anisotropy decay.

Proton-driven spin diffusion (PDSD) experiments in rotating solids have received a great deal of attention as a potential source of distance constraints in large biomolecules. However, the quantitative relationship between the molecular structure and observed spin diffusion has remained obscure due to the lack of an accurate theoretical description of the spin dynamics in these experiments. We start with presenting a detailed relaxation theory of PDSD in rotating solids that provides such a description. The theory applies to both conventional and radio-frequency-assisted PDSD experiments and extends to the non-Markovian regime to include such phenomena as rotational resonance (R(2)). The basic kinetic equation of the theory in the non-Markovian regime has the form of a memory function equation, with the role of the memory function played by the correlation function. The key assumption used in the derivation of this equation expresses the intuitive notion of the irreversible dissipation of coherences in macroscopic systems. Accurate expressions for the correlation functions and for the spin diffusion constants are given. The theory predicts that the spin diffusion constants governing the multi-site PDSD can be approximated by the constants observed in the two-site diffusion. Direct numerical simulations of PDSD dynamics via reversible Liouville-von Neumann equation are presented to support and compliment the theory. Remarkably, an exponential decay of the difference magnetization can be observed in such simulations in systems consisting of only 12 spins. This is a unique example of a real physical system whose typically macroscopic and apparently irreversible behavior can be traced via reversible microscopic dynamics. An accurate value for the spin diffusion constant can be usually obtained through direct simulations of PDSD in systems consisting of two (13)C nuclei and about ten (1)H nuclei from their nearest environment. Spin diffusion constants computed by this method are in excellent agreement with the spin diffusion constants obtained through equations given by the relaxation theory of PDSD. The constants resulting from these two approaches were also in excellent agreement with the results of 2D rotary resonance recoupling proton-driven spin diffusion (R(3)-PDSD) experiments performed in three model compounds, where magnetization exchange occurred over distances up to 4.9 A. With the methodology presented, highly accurate internuclear distances can be extracted from such data. Relayed transfer of magnetization between distant nuclei appears to be the main (and apparently resolvable) source of uncertainty in such measurements. The non-Markovian kinetic equation was applied to the analysis of the R(2) spin dynamics. The conventional semi-phenomenological treatment of relxation in R(2) has been shown to be equivalent to the assumption of the Lorentzian spectral density function in the relaxatoin theory of PDSD. As this assumption is a poor approximation in real physical systems, the conventional R(2) treatment is likely to carry a significant model error that has not been recognized previously. The relaxation theory of PDSD appears to provide an accurate, parameter-free alternative. Predictions of this theory agreed well with the full quantum mechanical simulations of the R(2) dynamics in the few simple model systems we considered.

NMR anisotropic parameters such as dipolar couplings and chemical shifts are central to structure and orientation determination of aligned membrane proteins and liquid crystals. Among the separated local field experiments, the proton evolved local field (PELF) scheme is particularly suitable to measure dynamically averaged dipolar couplings and give information on local molecular motions. However, the PELF experiment requires the acquisition of several 2D datasets at different mixing times to optimize the sensitivity for the complete range of dipolar couplings of the resonances in the spectrum. Here, we propose a new PELF experiment that takes the advantage of the Hadamard encoding (HE) to obtain higher sensitivity for a broad range of dipolar couplings using a single 2D experiment. The HE scheme is obtained by selecting the spin operators with phase switching of hard pulses. This approach enables one to detect four spin operators, simultaneously, which can be processed into two 2D spectra covering a broader range of dipolar couplings. The advantages of the new approach are illustrated for a U-(15)N NAL single crystal and the U-(15)N labeled single-pass membrane protein sarcolipin reconstituted in oriented lipid bicelles. The HE-PELF scheme can be implemented in other multidimensional experiments to speed up the characterization of the structure and dynamics of oriented membrane proteins and liquid crystalline samples.

General expressions relating the effects of pressure, temperature, and composition on solute association and conformational equilibria using the fluctuation theory of solutions are provided. The expressions are exact and can be used to interpret experimental or computer simulation data for any multicomponent mixture involving molecules of any size and character at any composition. The relationships involve particle-particle, particle-energy, and energy-energy correlations within local regions in the vicinity of each species involved in the equilibrium. In particular, it is demonstrated that the results can be used to study peptide and protein association or aggregation, protein denaturation, and protein-ligand binding. Exactly how the relevant fluctuating properties may be obtained from experimental or computer simulation data are also outlined. It is shown that the enthalpy, heat capacity, and compressibility differences associated with the equilibrium process can, in principle, be obtained from a single simulation. Fluctuation based expressions for partial molar heat capacities, thermal expansions, and isothermal compressibilities are also provided.