Circadian clocks go in vitro: purely post-translational oscillators in cyanobacteria

Recent findings about the core of the circadian oscillator in cyanobacteria are challenging the dogma that such clocks are driven through transcriptional–translational feedback regulation. Instead, the master pacemaker is independent of both transcription and translation, and consists of self-sustained oscillations in the phosphorylation status of the KaiC protein in vivo. Using a minimal cocktail of three recombinant proteins with adenosine triphosphate, the core clock was even reproduced in vitro. The so-born chemical oscillator could reproduce accurately temperature compensation and altered period phenotypes in mutants. This system now provides an ideal playground for rebuilding the circadian clock by adding successive components while understanding every single step with chemical resolution

Effects of the network structural properties on its controllability

In a recent paper, it has been suggested that the controllability of a diffusively coupled complex network, subject to localized feedback loops at some of its vertices, can be assessed by means of a Master Stability Function approach, where the network controllability is defined in terms of the spectral properties of an appropriate Laplacian matrix. Following that approach, a comparison study is reported here among different network topologies in terms of their controllability. The effects of heterogeneity in the degree distribution, as well as of degree correlation and community structure, are discussed.Comment: Also available online at: http://link.aip.org/link/?CHA/17/03310

Chimera states in heterogeneous networks

Chimera states in networks of coupled oscillators occur when some fraction of the oscillators synchronise with one another, while the remaining oscillators are incoherent. Several groups have studied chimerae in networks of identical oscillators, but here we study these states in a heterogeneous model for which the natural frequencies of the oscillators are chosen from a distribution. We obtain exact results by reduction to a finite set of differential equations. We find that heterogeneity can destroy chimerae, destroy all states except chimerae, or destabilise chimerae in Hopf bifurcations, depending on the form of the heterogeneity.Comment: Revised text. To appear, Chao

Radiative damping and synchronization in a graphene-based terahertz emitter

We investigate the collective electron dynamics in a recently proposed graphene-based terahertz emitter under the influence of the radiative damping effect, which is included self-consistently in a molecular dynamics approach. We show that under appropriate conditions synchronization of the dynamics of single electrons takes place, leading to a rise of the oscillating component of the charge current. The synchronization time depends dramatically on the applied dc electric field and electron scattering rate, and is roughly inversely proportional to the radiative damping rate that is determined by the carrier concentration and the geometrical parameters of the device. The emission spectra in the synchronized state, determined by the oscillating current component, are analyzed. The effective generation of higher harmonics for large values of the radiative damping strength is demonstrated.Comment: 9 pages, 7 figure

A "Cellular Neuronal" Approach to Optimization Problems

The Hopfield-Tank (1985) recurrent neural network architecture for the Traveling Salesman Problem is generalized to a fully interconnected "cellular" neural network of regular oscillators. Tours are defined by synchronization patterns, allowing the simultaneous representation of all cyclic permutations of a given tour. The network converges to local optima some of which correspond to shortest-distance tours, as can be shown analytically in a stationary phase approximation. Simulated annealing is required for global optimization, but the stochastic element might be replaced by chaotic intermittency in a further generalization of the architecture to a network of chaotic oscillators.Comment: -2nd revised version submitted to Chaos (original version submitted 6/07

Using synchronism of chaos for adaptive learning of network topology

In this paper we consider networks of dynamical systems that evolve in synchrony and investigate how dynamical information from the synchronization dynamics can be effectively used to learn the network topology, i.e., identify the time evolution of the couplings between the network nodes. To this aim, we present an adaptive strategy that, based on a potential that the network systems seek to minimize in order to maintain synchronization, can be successfully applied to identify the time evolution of the network from limited information. This strategy takes advantage of the properties of synchronism of chaos and of the presence of different communication delays over the network links. As a motivating example we consider a network of sensors surveying an area, in which information regarding the time evolution of the network connections can be used, e.g., to detect changes taking place within the area. We propose two different setups for our strategy. In the first one, synchronization has to be achieved at each node (as well as the identification of the couplings over the network links), based solely on a single scalar signal representing a superposition of signals from the other nodes in the network. In the second one, we incorporate an additional node, termed the maestro, having the function of maintaining network synchronization. We will see that when such an arrangement is realized, it will become possible to effectively identify the time evolution of networks that are much larger than would be possible in the absence of a maestro.Comment: 22 pages, 12 figures, accepted for publication on Physical Review

Transition to complete synchronization in phase coupled oscillators with nearest neighbours coupling

We investigate synchronization in a Kuramoto-like model with nearest neighbour coupling. Upon analyzing the behaviour of individual oscillators at the onset of complete synchronization, we show that the time interval between bursts in the time dependence of the frequencies of the oscillators exhibits universal scaling and blows up at the critical coupling strength. We also bring out a key mechanism that leads to phase locking. Finally, we deduce forms for the phases and frequencies at the onset of complete synchronization.Comment: 6 pages, 4 figures, to appear in CHAO

Exploring constrained quantum control landscapes

The broad success of optimally controlling quantum systems with external fields has been attributed to the favorable topology of the underlying control landscape, where the landscape is the physical observable as a function of the controls. The control landscape can be shown to contain no suboptimal trapping extrema upon satisfaction of reasonable physical assumptions, but this topological analysis does not hold when significant constraints are placed on the control resources. This work employs simulations to explore the topology and features of the control landscape for pure-state population transfer with a constrained class of control fields. The fields are parameterized in terms of a set of uniformly spaced spectral frequencies, with the associated phases acting as the controls. Optimization results reveal that the minimum number of phase controls necessary to assure a high yield in the target state has a special dependence on the number of accessible energy levels in the quantum system, revealed from an analysis of the first- and second-order variation of the yield with respect to the controls. When an insufficient number of controls and/or a weak control fluence are employed, trapping extrema and saddle points are observed on the landscape. When the control resources are sufficiently flexible, solutions producing the globally maximal yield are found to form connected `level sets' of continuously variable control fields that preserve the yield. These optimal yield level sets are found to shrink to isolated points on the top of the landscape as the control field fluence is decreased, and further reduction of the fluence turns these points into suboptimal trapping extrema on the landscape. Although constrained control fields can come in many forms beyond the cases explored here, the behavior found in this paper is illustrative of the impacts that constraints can introduce.Comment: 10 figure

Aspect ratio dependence of heat transfer and large-scale flow in turbulent convection

The heat transport and corresponding changes in the large-scale circulation (LSC) in turbulent Rayleigh-B\'{e}nard convection are studied by means of three-dimensional direct numerical simulations as a function of the aspect ratio $\Gamma$ of a closed cylindrical cell and the Rayleigh number $Ra$. For small and moderate aspect ratios, the global heat transfer law $Nu=A\times Ra^{\beta}$ shows a power law dependence of both fit coefficients $A$ and $\beta$ on the aspect ratio. A minimum Nusselt number coincides with the point where the LSC undergoes a transition from a single-roll to a double-roll pattern. With increasing aspect ratio, we detect complex multi-roll LSC configurations. The aspect ratio dependence of the turbulent heat transfer for small and moderate $\Gamma$ is in line with a varying amount of energy contained in the LSC, as quantified by the Proper Orthogonal Decomposition analysis. For $\Gamma\gtrsim 8$ the heat transfer becomes independent of the aspect ratio.Comment: 17 pages, 11 Postscript figures (in parts downscaled), accepted for J. Fluid Mec