Networks of nonlinear superconducting transmission line resonators

We investigate a network of coupled superconducting transmission line resonators, each of them made nonlinear with a capacitively shunted Josephson junction coupling to the odd flux modes of the resonator. The resulting eigenmode spectrum shows anticrossings between the plasma mode of the shunted junction and the odd resonator modes. Notably, we find that the combined device can inherit the complete nonlinearity of the junction, allowing for a description as a harmonic oscillator with a Kerr nonlinearity. Using a dc SQUID instead of a single junction, the nonlinearity can be tuned between 10 kHz and 4 MHz while maintaining resonance frequencies of a few gigahertz for realistic device parameters. An array of such nonlinear resonators can be considered a scalable superconducting quantum simulator for a Bose-Hubbard Hamiltonian. The device would be capable of accessing the strongly correlated regime and be particularly well suited for investigating quantum many-body dynamics of interacting particles under the influence of drive and dissipation.Comment: 18 pages, 3 figure

Inhibition of matrix metalloproteinases attenuates brain damage in experimental meningococcal meningitis

Background: Approximately 7% of survivors from meningococcal meningitis (MM) suffer from neurological sequelae due to brain damage in the course of meningitis. The present study focuses on the role of matrix metalloproteinases (MMPs) in a novel mouse model of MM-induced brain damage. Methods: The model is based on intracisternal infection of BALB/c mice with a serogroup C Neisseria meningitidis strain. Mice were infected with meningococci and randomised for treatment with the MMP inhibitor batimastat (BB-94) or vehicle. Animal survival, brain injury and host-response biomarkers were assessed 48 h after meningococcal challenge. Results: Mice that received BB-94 presented significantly diminished MMP-9 levels (p < 0.01), intracerebral bleeding (p < 0.01), and blood brain barrier (BBB) breakdown (p < 0.05) in comparison with untreated animals. In mice suffering from MM, the amount of MMP- 9 measured by zymography significantly correlated with both intracerebral haemorrhage (p < 0.01) and BBB disruption (p < 0.05). Conclusions: MMPs significantly contribute to brain damage associated with experimental MM. Inhibition of MMPs reduces intracranial complications in mice suffering from MM, representing a potential adjuvant strategy in MM post-infection sequelae

Mesoscopic mean-field theory for spin-boson chains in quantum optical systems

We present a theoretical description of a system of many spins strongly coupled to a bosonic chain. We rely on the use of a spin-wave theory describing the Gaussian fluctuations around the mean-field solution, and focus on spin-boson chains arising as a generalization of the Dicke Hamiltonian. Our model is motivated by experimental setups such as trapped ions, or atoms/qubits coupled to cavity arrays. This situation corresponds to the cooperative (E⊗β) Jahn-Teller distortion studied in solid-state physics. However, the ability to tune the parameters of the model in quantum optical setups opens up a variety of novel intriguing situations. The main focus of this paper is to review the spin-wave theoretical description of this problem as well as to test the validity of mean-field theory. Our main result is that deviations from mean-field effects are determined by the interplay between magnetic order and mesoscopic cooperativity effects, being the latter strongly size-dependent

Arrays of waveguide-coupled optical cavities that interact strongly with atoms

We describe a realistic scheme for coupling atoms or other quantum emitters with an array of coupled optical cavities. We consider open Fabry-Perot microcavities coupled to the emitters. Our central innovation is to connect the microcavities to waveguide resonators, which are in turn evanescently coupled to each other on a photonic chip to form a coupled cavity chain. In this paper, we describe the components, their technical limitations and the factors that need to be determined experimentally. This provides the basis for a detailed theoretical analysis of two possible experiments to realize quantum squeezing and controlled quantum dynamics. We close with an outline of more advanced applications.Comment: 30 pages, 8 figures. Submitted to New Journal of Physic

Quantum Statistics and Entanglement of Two Electromagnetic Field Modes Coupled via a Mesoscopic SQUID Ring

In this paper we investigate the behaviour of a fully quantum mechanical system consisting of a mesoscopic SQUID ring coupled to one or two electromagnetic field modes. We show that we can use a static magnetic flux threading the SQUID ring to control the transfer of energy, the entanglement and the statistical properties of the fields coupled to the ring. We also demonstrate that at, and around, certain values of static flux the effective coupling between the components of the system is large. The position of these regions in static flux is dependent on the energy level structure of the ring and the relative field mode frequencies, In these regions we find that the entanglement of states in the coupled system, and the energy transfer between its components, is strong.Comment: 15 pages, 19 figures, Uploaded as implementing a policy of arXiving old paper

A transcribed enhancer dictates mesendoderm specification in pluripotency.

Enhancers and long noncoding RNAs (lncRNAs) are key determinants of lineage specification during development. Here, we evaluate remodeling of the enhancer landscape and modulation of the lncRNA transcriptome during mesendoderm specification. We sort mesendodermal progenitors from differentiating embryonic stem cells (ESCs) according to Eomes expression, and find that enhancer usage is coordinated with mesendoderm-specific expression of key lineage-determining transcription factors. Many of these enhancers are associated with the expression of lncRNAs. Examination of ESC-specific enhancers interacting in three-dimensional space with mesendoderm-specifying transcription factor loci identifies MesEndoderm Transcriptional Enhancer Organizing Region (Meteor). Genetic and epigenetic manipulation of the Meteor enhancer reveal its indispensable role during mesendoderm specification and subsequent cardiogenic differentiation via transcription-independent and -dependent mechanisms. Interestingly, Meteor-deleted ESCs are epigenetically redirected towards neuroectodermal lineages. Loci, topologically associating a transcribed enhancer and its cognate protein coding gene, appear to represent therefore a class of genomic elements controlling developmental competence in pluripotency

Pneumococcal meningitis: Clinical-pathological correlations (meningene-path)

Pneumococcal meningitis is associated with substantial mortality and morbidity. We systematically assessed brain histopathology of 31 patients who died of pneumococcal meningitis from a nationwide study (median age 67 years; 21 (67 %) were male) using a pathology score including inflammation and vascular damage. Of the 27 patients with known time from the admission to death, 14 patients died within 7 days of admission and 13 after 7 days of admission. Eleven of 25 (44 %) patients had been treated with adjunctive dexamethasone therapy. Observed pathological processes were inflammation of medium-large arteries in 30 brains (97 %), cerebral haemorrhage in 24 (77 %), cerebritis in 24 (77 %), thrombosis in 21 (68 %), infarction in 19 (61 %) and ventriculitis in 19 (of 28 cases, 68 %). Inflammation of medium-large arteries led to obstruction of the vascular lumen in 14 (of 31 cases, 45 %). Vascular inflammation was associated with infarction and thrombosis of brain parenchymal vessels. Hippocampal dentate gyrus apoptosis between patients treated with and without dexamethasone was similar (p = 0.66); however, dexamethasone treated patients had higher total pathology score than non-dexamethasone treated patients (p = 0.003). Our study shows that vascular damage is key in the process of brain damage in pneumococcal meningitis. Data and material of this study will be made open-access for translational research in pneumococcal meningitis (MeninGene-Path)

Molecular characterization of Miraflores peach variety and relatives using SSRs

The definitive version is published in: http://www.sciencedirect.com/science/journal/03044238Some traditional peach varieties, originated from the region of Aragón (Spain), were analysed by SSRs (Simple Sequence Repeats). The aim of this research was to characterize 19 clones related to ‘Miraflores’ variety, with unknown pedigrees, to assess their genetic diversity and to elucidate their possible relationships with 10 traditional peach varieties. Twenty SSR primer pairs with high levels of polymorphism, which have been previously developed for peach, were used in this study. A total of 46 alleles were obtained for all the microsatellites studied, ranging from one to six alleles per locus, with a mean value of 2.3 alleles per locus. Fourteen SSRs were polymorphic in the set of varieties studied and permitted to distinguish 16 different genotypes out of the 30 initially studied, although fourteen ‘Miraflores’ clones showed identical gel profiles. The genetic distance matrix was used to construct Neighbor joining cluster and to perform principal coordinate analysis which allowed the arrangement of all the genotypes according to their genetic relationships. The genetic relationships among these traditional peach varieties, and in particular among ‘Miraflores’ clones are discussed. The obtained results confirm that microsatellite markers are very useful for these purposes.We are thankful to T.N. Zhebentyayeva and G.L. Reighard for helpful comments on the manuscript. This research was funded by CICYT (Comisión Interministerial de Ciencia y Tecnología, AGL2002-04219 and AGL 2005-05533), INIA (Instituto Nacional de Investigación y Tecnología Agraria y Alimentación, RF03-014-C2), Bilateral Spain-France (HF03-273) and DGA (A28, A44) projects and co-funded by the European Regional Development Fund. M. Bouhadida was supported by a fellowship from the AECI (Agencia Española de Cooperación Internacional) of the Spanish Ministry of Foreign Affairs.Peer reviewe

Out-of-equilibrium physics in driven dissipative coupled resonator arrays

Coupled resonator arrays have been shown to exhibit interesting many- body physics including Mott and Fractional Hall states of photons. One of the main differences between these photonic quantum simulators and their cold atoms coun- terparts is in the dissipative nature of their photonic excitations. The natural equi- librium state is where there are no photons left in the cavity. Pumping the system with external drives is therefore necessary to compensate for the losses and realise non-trivial states. The external driving here can easily be tuned to be incoherent, coherent or fully quantum, opening the road for exploration of many body regimes beyond the reach of other approaches. In this chapter, we review some of the physics arising in driven dissipative coupled resonator arrays including photon fermionisa- tion, crystallisation, as well as photonic quantum Hall physics out of equilibrium. We start by briefly describing possible experimental candidates to realise coupled resonator arrays along with the two theoretical models that capture their physics, the Jaynes-Cummings-Hubbard and Bose-Hubbard Hamiltonians. A brief review of the analytical and sophisticated numerical methods required to tackle these systems is included.Comment: Chapter that appeared in "Quantum Simulations with Photons and Polaritons: Merging Quantum Optics with Condensed Matter Physics" edited by D.G.Angelakis, Quantum Science and Technology Series, Springer 201