Reconstructing the quantum state of oscillator networks with a single qubit

We introduce a scheme to reconstruct arbitrary states of networks composed of quantum oscillators-e. g., the motionalstate of trapped ions or the radiation state of coupled cavities. The scheme involves minimal resources and minimal access, in the sense that it (i) requires only the interaction between a one-qubit probe and a single node of the network; (ii) provides the Weyl characteristic function of the network directly from the data, avoiding any tomographic transformation; (iii) involves the tuning of only one coupling parameter. In addition, we show that a number of quantum properties can be extracted without full reconstruction of the state. The scheme can be used for probing quantum simulations of anharmonic many-body systems and quantum computations with continuous variables. Experimental implementation with trapped ions is also discussed and shown to be within reach of current technology.

Chaotic synchronization in general network topology for scene segmentation

Chaotic synchronization has been discovered to be an important property of neural activities, which in turn has encouraged many researchers to develop chaotic neural networks for scene and data analysis. In this paper, we study the synchronization role of coupled chaotic oscillators in networks of general topology. Specifically, a rigorous proof is presented to show that a large number of oscillators with arbitrary geometrical connections can be synchronized by providing a sufficiently strong coupling strength. Moreover, the results presented in this paper not only are valid to a wide class of chaotic oscillators, but also cover the parameter mismatch case. Finally, we show how the obtained result can be applied to construct an oscillatory network for scene segmentation.

Cellular and network mechanisms of rhythm generation in spinal cord circuits

The generation of rhythmic electrical activity is a prominent feature of spinal cord circuits that is used for locomotion and also for circuit refinement during development. The mechanisms involved in rhythm generation in spinal cord networks are not fully understood. It is for example not known whether spinal cord rhythms are driven by pacemaker neurons and if yes, which neurons are involved in this function. We studied the mechanisms involved in rhythm generation in slice cultures from fetal rats that were grown on multielectrode arrays (MEAs). We combined multisite extracellular recordings from the MEA electrodes with intracellular patch clamp recordings from single neurons. We found that spatially restricted oscillations of activity appeared in most of the cultures spontaneously. Such activity was based on intrinsic activity in a percentage of the neurons that could activate the spinal networks through recurrent excitation. The local oscillator networks critically involved NMDA, AMPA and GABA / glycine receptors at subsequent phases of the oscillation cycle. Intrinsic spiking in individual neurons (in the absence of functional synaptic coupling) was based on persistent sodium currents. Intrinsic firing as well as persistent sodium currents were increased by 5-HT through 5-HT2 receptors. Comparing neuronal activity to muscle activity in co-cultures of spinal cord slices with muscle fibers we found that a percentage of the intrinsically spiking neurons were motoneurons. These motoneurons were electrically coupled among each other and they could drive the spinal networks through cholinergic recurrent excitation. These findings open the possibility that during development rhythmic activity in motoneurons is not only involved in circuit refinement downstream at the neuromuscular endplates but also upstream at the level of spinal cord circuits.

Frustration induced oscillator death on networks

An array of identical maps with Ising symmetry, with both positive and negative couplings, is studied. We divide the maps into two groups, with positive intra-group couplings and negative inter-group couplings. This leads to antisynchronization between the two groups which have the same stability properties as the synchronized state. Introducing a certain degree of randomness in signs of these couplings destabilizes the anti-synchronized state. Further increasing the randomness in signs of these couplings leads to oscillator death. This is essentially a frustration induced phenomenon. We explain the observed results using the theory of random matrices with nonzero mean. We briefly discuss applications to coupled differential equations. (C) 2013 AIP Publishing LLC.

Programming chemical kinetics: engineering dynamic reaction networks with DNA strand displacement

Over the last century, the silicon revolution has enabled us to build faster, smaller and more sophisticated computers. Today, these computers control phones, cars, satellites, assembly lines, and other electromechanical devices. Just as electrical wiring controls electromechanical devices, living organisms employ "chemical wiring" to make decisions about their environment and control physical processes. Currently, the big difference between these two substrates is that while we have the abstractions, design principles, verification and fabrication techniques in place for programming with silicon, we have no comparable understanding or expertise for programming chemistry.

In this thesis we take a small step towards the goal of learning how to systematically engineer prescribed non-equilibrium dynamical behaviors in chemical systems. We use the formalism of chemical reaction networks (CRNs), combined with mass-action kinetics, as our programming language for specifying dynamical behaviors. Leveraging the tools of nucleic acid nanotechnology (introduced in Chapter 1), we employ synthetic DNA molecules as our molecular architecture and toehold-mediated DNA strand displacement as our reaction primitive.

Abstraction, modular design and systematic fabrication can work only with well-understood and quantitatively characterized tools. Therefore, we embark on a detailed study of the "device physics" of DNA strand displacement (Chapter 2). We present a unified view of strand displacement biophysics and kinetics by studying the process at multiple levels of detail, using an intuitive model of a random walk on a 1-dimensional energy landscape, a secondary structure kinetics model with single base-pair steps, and a coarse-grained molecular model that incorporates three-dimensional geometric and steric effects. Further, we experimentally investigate the thermodynamics of three-way branch migration. Our findings are consistent with previously measured or inferred rates for hybridization, fraying, and branch migration, and provide a biophysical explanation of strand displacement kinetics. Our work paves the way for accurate modeling of strand displacement cascades, which would facilitate the simulation and construction of more complex molecular systems.

In Chapters 3 and 4, we identify and overcome the crucial experimental challenges involved in using our general DNA-based technology for engineering dynamical behaviors in the test tube. In this process, we identify important design rules that inform our choice of molecular motifs and our algorithms for designing and verifying DNA sequences for our molecular implementation. We also develop flexible molecular strategies for "tuning" our reaction rates and stoichiometries in order to compensate for unavoidable non-idealities in the molecular implementation, such as imperfectly synthesized molecules and spurious "leak" pathways that compete with desired pathways.

We successfully implement three distinct autocatalytic reactions, which we then combine into a de novo chemical oscillator. Unlike biological networks, which use sophisticated evolved molecules (like proteins) to realize such behavior, our test tube realization is the first to demonstrate that Watson-Crick base pairing interactions alone suffice for oscillatory dynamics. Since our design pipeline is general and applicable to any CRN, our experimental demonstration of a de novo chemical oscillator could enable the systematic construction of CRNs with other dynamic behaviors.

Robustness and Coherence of a Three-Protein Circadian Oscillator: Landscape and Flux Perspectives

Three-protein circadian oscillations in cyanobacteria sustain for weeks. To understand how cellular oscillations function robustly in stochastic fluctuating environments, we used a stochastic model to uncover two natures of circadian oscillation: the potential landscape related to steady-state probability distribution of protein concentrations; and the corresponding flux related to speed of concentration changes which drive the oscillations. The barrier height of escaping from the oscillation attractor on the landscape provides a quantitative measure of the robustness and coherence for oscillations against intrinsic and external fluctuations. The difference between the locations of the zero total driving force and the extremal of the potential provides a possible experimental probe and quantification of the force from curl flux. These results, correlated with experiments, can help in the design of robust oscillatory networks.

Broadband chaos generated by an optoelectronic oscillator.

We study an optoelectronic time-delay oscillator that displays high-speed chaotic behavior with a flat, broad power spectrum. The chaotic state coexists with a linearly stable fixed point, which, when subjected to a finite-amplitude perturbation, loses stability initially via a periodic train of ultrafast pulses. We derive approximate mappings that do an excellent job of capturing the observed instability. The oscillator provides a simple device for fundamental studies of time-delay dynamical systems and can be used as a building block for ultrawide-band sensor networks.

When long-range zero-lag synchronization is feasible in cortical networks

Many studies have reported long-range synchronization of neuronal activity between brain areas, in particular in the beta and gamma bands with frequencies in the range of 14–30 and 40–80 Hz, respectively. Several studies have reported synchrony with zero phase lag, which is remarkable considering the synaptic and conduction delays inherent in the connections between distant brain areas. This result has led to many speculations about the possible functional role of zero-lag synchrony, such as for neuronal communication, attention, memory, and feature binding. However, recent studies using recordings of single-unit activity and local field potentials report that neuronal synchronization may occur with non-zero phase lags. This raises the questions whether zero-lag synchrony can occur in the brain and, if so, under which conditions. We used analytical methods and computer simulations to investigate which connectivity between neuronal populations allows or prohibits zero-lag synchrony. We did so for a model where two oscillators interact via a relay oscillator. Analytical results and computer simulations were obtained for both type I Mirollo–Strogatz neurons and type II Hodgkin–Huxley neurons. We have investigated the dynamics of the model for various types of synaptic coupling and importantly considered the potential impact of Spike-Timing Dependent Plasticity (STDP) and its learning window. We confirm previous results that zero-lag synchrony can be achieved in this configuration. This is much easier to achieve with Hodgkin–Huxley neurons, which have a biphasic phase response curve, than for type I neurons. STDP facilitates zero-lag synchrony as it adjusts the synaptic strengths such that zero-lag synchrony is feasible for a much larger range of parameters than without STDP.

Chaotic phase synchronization and desynchronization in an oscillator network for object selection

Object selection refers to the mechanism of extracting objects of interest while ignoring other objects and background in a given visual scene. It is a fundamental issue for many computer vision and image analysis techniques and it is still a challenging task to artificial Visual systems. Chaotic phase synchronization takes place in cases involving almost identical dynamical systems and it means that the phase difference between the systems is kept bounded over the time, while their amplitudes remain chaotic and may be uncorrelated. Instead of complete synchronization, phase synchronization is believed to be a mechanism for neural integration in brain. In this paper, an object selection model is proposed. Oscillators in the network representing the salient object in a given scene are phase synchronized, while no phase synchronization occurs for background objects. In this way, the salient object can be extracted. In this model, a shift mechanism is also introduced to change attention from one object to another. Computer simulations show that the model produces some results similar to those observed in natural vision systems.

Storing quantum states in bosonic dissipative networks

By considering a network of dissipative quantum harmonic oscillators, we deduce and analyse the optimum topologies which are able to store quantum superposition states, protecting them from decoherence, for the longest period of time. The storage is made dynamically, in that the states to be protected evolve through the network before being retrieved back in the oscillator where they were prepared. The decoherence time during the dynamic storage process is computed and we demonstrate that it is proportional to the number of oscillators in the network for a particular regime of parameters.

Radial basis function network applied to the linearization of a voltage controlled oscillator

An analog circuit that implements a radial basis function network is presented. The proposed circuit allows the adjustment of all shape parameters of the radial functions, i.e., amplitude, center and width. The implemented network was applied to the linearization of a nonlinear circuit, a voltage controlled oscillator (VCO). This application can be classified as an open-loop control in which the network plays the role of the controller. Experimental results have proved the linearization capability of the proposed circuit. Its performance can be improved by using a network with more basis functions. Copyright 2007 ACM.

Experimental Assessment of the Sensitiveness of an Electrochemical Oscillator towards Chemical Perturbations

In this study we address the problem of the response of a (electro)chemical oscillator towards chemical perturbations of different magnitudes. The chemical perturbation was achieved by addition of distinct amounts of trifluoromethanesulfonate (TFMSA), a rather stable and non-specifically adsorbing anion, and the system under investigation was the methanol electro-oxidation reaction under both stationary and oscillatory regimes. Increasing the anion concentration resulted in a decrease in the reaction rates of methanol oxidation and a general decrease in the parameter window where oscillations occurred. Furthermore, the addition of TFMSA was found to decrease the induction period and the total duration of oscillations. The mechanism underlying these observations was derived mathematically and revealed that inhibition in the methanol oxidation through blockage of active sites was found to further accelerate the intrinsic non-stationarity of the unperturbed system. Altogether, the presented results are among the few concerning the experimental assessment of the sensitiveness of an oscillator towards chemical perturbations. The universal nature of the complex chemical oscillator investigated here might be used for reference when studying the dynamics of other less accessible perturbed networks of (bio)chemical reactions.

Architectures, stability and optimization for clock distribution networks

Synchronous telecommunication networks, distributed control systems and integrated circuits have its accuracy of operation dependent on the existence of a reliable time basis signal extracted from the line data stream and acquirable to each node. In this sense, the existence of a sub-network (inside the main network) dedicated to the distribution of the clock signals is crucially important. There are different solutions for the architecture of the time distribution sub-network and choosing one of them depends on cost, precision, reliability and operational security. In this work we expose: (i) the possible time distribution networks and their usual topologies and arrangements. (ii) How parameters of the network nodes can affect the reachability and stability of the synchronous state of a network. (iii) Optimizations methods for synchronous networks which can provide low cost architectures with operational precision, reliability and security. (C) 2011 Elsevier B. V. All rights reserved.

Low-loss waveguides fabricated by femtosecond chirped-pulse oscillator

Recent results on direct femtosecond inscription of straight low-loss waveguides in borosilicate glass are presented. We also demonstrate lowest ever losses in curvilinear waveguides, which we use as main building blocks for integrated photonics circuits. Low-loss waveguides are of great importance to a variety of applications of integrated optics. We report on recent results of direct femtosecond fabrication of smooth low-loss waveguides in standard optical glass by means of femtosecond chirped-pulse oscillator only (Scientific XL, Femtolasers), operating at the repetition rate of 11 MHz, at the wavelength of 800 nm, with FWHM pulse duration of about 50 fs, and a spectral widths of 30 nm. The pulse energy on target was up to 70 nJ. In transverse inscription geometry, we inscribed waveguides at the depth from 10 to 300 micrometers beneath the surface in the samples of 50 x 50 x 1 mm dimensions made of pure BK7 borosilicate glass. The translation of the samples accomplished by 2D air-bearing stage (Aerotech) with sub-micrometer precision at a speed of up to 100 mm per second (hardware limit). Third direction of translation (Z-, along the inscribing beam or perpendicular to sample plane) allows truly 3D structures to be fabricated. The waveguides were characterized in terms of induced refractive index contrast, their dimensions and cross-sections, mode-field profiles, total insertion losses at both 633 nm and 1550 nm. There was almost no dependence on polarization for the laser inscription. The experimental conditions – depth, laser polarization, pulse energy, translation speed and others, were optimized for minimum insertion losses when coupled to a standard optical fibre SMF-28. We found coincidence of our optimal inscription conditions with recently published by other groups [1, 3] despite significant difference in practically all experimental parameters. Using optimum regime for straight waveguides fabrication, we inscribed a set of curvilinear tracks, which were arranged in a way to ensure the same propagation length (and thus losses) and coupling conditions, while radii of curvature varied from 3 to 10 mm. This allowed us to measure bend-losses – they less than or about 1 dB/cm at R=10 mm radius of curvature. We also demonstrate a possibility to fabricate periodical perturbations of the refractive index in such waveguides with the periods using the same set-up. We demonstrated periods of about 520 nm, which allowed us to fabricate wavelength-selective devices using the same set-up. This diversity as well as very short time for inscription (the optimum translation speed was found to be 40 mm/sec) makes our approach attractive for industrial applications, for example, in next generation high-speed telecom networks.

Low-loss waveguides fabricated by femtosecond chirped-pulse oscillator

Recent results on direct femtosecond inscription of straight low-loss waveguides in borosilicate glass are presented. We also demonstrate lowest ever losses in curvilinear waveguides, which we use as main building blocks for integrated photonics circuits. Low-loss waveguides are of great importance to a variety of applications of integrated optics. We report on recent results of direct femtosecond fabrication of smooth low-loss waveguides in standard optical glass by means of femtosecond chirped-pulse oscillator only (Scientific XL, Femtolasers), operating at the repetition rate of 11 MHz, at the wavelength of 800 nm, with FWHM pulse duration of about 50 fs, and a spectral widths of 30 nm. The pulse energy on target was up to 70 nJ. In transverse inscription geometry, we inscribed waveguides at the depth from 10 to 300 micrometers beneath the surface in the samples of 50 x 50 x 1 mm dimensions made of pure BK7 borosilicate glass. The translation of the samples accomplished by 2D air-bearing stage (Aerotech) with sub-micrometer precision at a speed of up to 100 mm per second (hardware limit). Third direction of translation (Z-, along the inscribing beam or perpendicular to sample plane) allows truly 3D structures to be fabricated. The waveguides were characterized in terms of induced refractive index contrast, their dimensions and cross-sections, mode-field profiles, total insertion losses at both 633 nm and 1550 nm. There was almost no dependence on polarization for the laser inscription. The experimental conditions – depth, laser polarization, pulse energy, translation speed and others, were optimized for minimum insertion losses when coupled to a standard optical fibre SMF-28. We found coincidence of our optimal inscription conditions with recently published by other groups [1, 3] despite significant difference in practically all experimental parameters. Using optimum regime for straight waveguides fabrication, we inscribed a set of curvilinear tracks, which were arranged in a way to ensure the same propagation length (and thus losses) and coupling conditions, while radii of curvature varied from 3 to 10 mm. This allowed us to measure bend-losses – they less than or about 1 dB/cm at R=10 mm radius of curvature. We also demonstrate a possibility to fabricate periodical perturbations of the refractive index in such waveguides with the periods using the same set-up. We demonstrated periods of about 520 nm, which allowed us to fabricate wavelength-selective devices using the same set-up. This diversity as well as very short time for inscription (the optimum translation speed was found to be 40 mm/sec) makes our approach attractive for industrial applications, for example, in next generation high-speed telecom networks.