100 research outputs found

    Phase Dynamics of Two Entangled Qubits

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    We make a geometric study of the phases acquired by a general pure bipartite two level system after a cyclic unitary evolution. The geometric representation of the two particle Hilbert space makes use of Hopf fibrations. It allows for a simple description of the dynamics of the entangled state's phase during the whole evolution. The global phase after a cyclic evolution is always an entire multiple of π\pi for all bipartite states, a result that does not depend on the degree of entanglement. There are three different types of phases combining themselves so as to result in the nπn \pi global phase. They can be identified as dynamical, geometrical and topological. Each one of them can be easily identified using the presented geometric description. The interplay between them depends on the initial state and on its trajectory and the results obtained are shown to be in connection to those on mixed states phases.Comment: 9 figures, slightly different version from the accepted on

    Geometrical organization of solutions to random linear Boolean equations

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    The random XORSAT problem deals with large random linear systems of Boolean variables. The difficulty of such problems is controlled by the ratio of number of equations to number of variables. It is known that in some range of values of this parameter, the space of solutions breaks into many disconnected clusters. Here we study precisely the corresponding geometrical organization. In particular, the distribution of distances between these clusters is computed by the cavity method. This allows to study the `x-satisfiability' threshold, the critical density of equations where there exist two solutions at a given distance.Comment: 20 page

    Genetic engineering of Escherichia coli to produce a 1:1 complex of the Anabaena sp. PCC 7120 nuclease NucA and its inhibitor NuiA

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    A series of T7-promoter based bicistronic expression vectors was constructed in order to produce the complex of the Anabaena sp. PCC 7120 DNA/RNA non-specific nuclease NucA and its inhibitor NuiA. With all constructs, tandem expression of nucA and nuiA results in aggregation and inclusion body formation of NucA, independent of the order of the genes, the relative expression of the two proteins and the temperature applied during expression. Two constructs in which nuiA is the first and nucA the second cistron lead to an approximately one order of magnitude higher expression of nuiA compared with nucA. In these cells inclusion bodies are formed which contain NucA and NuiA in a 1:1 molar ratio. The complex can be solubilized with 6 M urea after disruption of the cells by sonication, renatured by dialysis and purified to homogeneity. 2 mg of the complex are obtained from 1:1 Escherichia coli culture. As shown by gel filtration and analytical ultracentrifugation, our system leads to a highly pure and homogeneous complex preparation, as required for biophysical and structural studies. Thus, our new method is a superior alternative for the production of the NucA/NuiA complex in which separately produced nuclease and inhibitor are mixed, and an excess of one or the other component, as well as aggregates of NucA, have to be removed from the preparation. (C) 2000 Elsevier Science B.V

    Biochemical characterization of Anabaena sp. strain PCC 7120 non- specific nuclease NucA and its inhibitor NuiA

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    We have established overexpression systems and purification protocols for NucA and NuiA, a sugar non-specific nuclease and its protein inhibitor from Anabaena sp. strain PCC 7120, in order to characterize these proteins in detail. CD spectroscopy revealed that NucA has a similar secondary-structure composition, 13% a helix and 20% β sheet, to the related Serratia nuclease, while NuiA represents a protein with a higher α-helical (29%) and β-sheet (24%) content than NucA. Denaturation experiments showed that the stabilities of NucA and NuiA are in the typical range for proteins of mesophilic organisms, NuiA with ΔG(o)(H2O)= 63.4 J* mol-1, (residue), being slightly more stable than its target NucA with ΔΔ(o)(H2O)= 46.3 J * mol- 1(residue). The nuclease requires divalent metal ions as cofactors, the optimum concentration being around 5 mM for Mn2+ or Mg2+. The order of effectiveness of various divalent cations to function as cofactors for the hydrolytic activity of NucA is Mn2+ = Co2+ > Mg2+≤ Ni2+> Ca2+ = Cd2+ at a concentration of 5 mM. Nuclease activity decreases with increasing concentration of monovalent salt. The activity of NucA shows a pH optimum at pH 5.5-7.5. The temperature optimum is around 35°C, the activation energy was calculated to be 53 kJ mol-1. The specific activity of the nuclease towards high molecular-mass DNA is 8.4X 106 Kunitz-units * mg-1, which means that NucA is one of the most active nucleases known. Kinetic constants for the cleavage of various DNA and RNA substrates by NucA are all in the range K(m) ≤ 0.1 mg * ml- and k(cm) 1000 s-1. As other non-specific nucleases, NucA exhibits sequence preferences, similar to the related Serratia nuclease, NucA avoids cleavage of d(A) d(T) tracts. The nucleolytic activity of NucA is completely inhibited at equimolar concentrations of nuclease and inhibitor. An ultracentrifugation analysis showed that NucA and NuiA form a 1:1 complex. The interaction of NucA with NuiA was also investigated by CD spectroscopy and revealed no major conformational changes upon complex formation of the two proteins

    Genetic engineering, production and characterisation of monomeric variants of the dimeric Serratia marcescens endonuclease

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    The Serratia nuclease is a non-specific endonuclease which cleaves single- and double-stranded RNA and DNA. It is a member of a large family of related endonucleases, most of which fire dimers of identical subunits, with the notable exception of the Anabaena nuclease which is a monomer. In order to find out whether the dimer state of the Serratia nuclease is essential for its function we have produced variants of this nuclease which based on the crystal structure (Miller, M.D. and Krause, K.L. (1996), Protein Science 5, 24-33) were expected to be unable to dimerise. We demonstrate here that these variants, H184A, H1184N, H184T and H184R, are monomers and have the same secondary structure, stability towards chemical denaturation and activity as the wild-type enzyme. This allows to conclude that the dimeric state is not essential for the catalytic function of the Serratia nuclease. In contrast, the S179C variant which is also a monomer shows little activity, presumably because this amino acid substitution changes the structure of the enzyme

    Achievable rates for the Gaussian quantum channel

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    We study the properties of quantum stabilizer codes that embed a finite-dimensional protected code space in an infinite-dimensional Hilbert space. The stabilizer group of such a code is associated with a symplectically integral lattice in the phase space of 2N canonical variables. From the existence of symplectically integral lattices with suitable properties, we infer a lower bound on the quantum capacity of the Gaussian quantum channel that matches the one-shot coherent information optimized over Gaussian input states.Comment: 12 pages, 4 eps figures, REVTe

    Kinetic analysis of the cleavage of natural and synthetic substrates by the Serratia nuclease

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    The extracellular nuclease from Serratia marcescens is a non-specific endonuclease that hydrolyzes double-stranded and single-stranded DNA and RNA with high specific activity. Steady-state and pre-steady-state kinetic cleavage experiments were performed with natural and synthetic DNA and RNA substrates to understand the mechanism of action of the Serratia nuclease. Most of the natural substrates are cleaved with similar k(cat) and K(m) values, the k(cat)/K(m) ratios being comparable to that of staphylococcal nuclease. Substrates with extreme structural features, like poly(dA) · poly(dT) or poly(dG) · poly(dC), are cleaved by the Serratia nuclease with a 50 times higher or 10 times lower K(m), respectively, as salmon testis DNA. Neither with natural DNA or RNA nor synthetic oligodeoxynucleotide substrates did we observe substrate inhibition for the Serratia nuclease as reported recently. Experiments with short oligodeoxynucleotides confirmed previous results that for moderately good cleavage activity the substrate should contain at least five phosphate residues. Shorter substrates are still cleaved by the Serratia nuclease, albeit at a rate reduced by a factor of more than 100. Cleavage experiments with oligodeoxynucleotides substituted by a single phosphorothioate group showed that the negative charge of the proR(p)-oxygen of the phosphate group 3' adjacent to the scissile phosphodiester bond is essential for cleavage, as only the R(p)-phosphorothioate supports cleavage at the 5' adjacent phosphodiester bond. Furthermore, the modified bond itself is only cleaved in the R(p)-diastereomer, albeit 1000 times more slowly than the corresponding unmodified phosphodiester bond, which offers the possibility to determine the stereochemical outcome of cleavage. Pre-steady-state cleavage experiments demonstrate that it is not dissociation of products but association of enzyme and substrate or the cleavage of the phosphodiester bond that is the rate-limiting step of the reaction. Finally, it is shown that Serratia nuclease accepts thymidine 3',5'-bis(p-nitrophenyl)phosphate as a substrate and cleaves it at its 5'-end to produce nitrophenol and thymidine 3'-(p-nitrophenylphosphate) 5-phosphate. The rate of cleavage of this artificial substrate, however, is 6-7 orders of magnitude smaller than the rate of cleavage of macromolecular DNA or RNA

    Device-Independent Quantum Key Distribution

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    Cryptographic key exchange protocols traditionally rely on computational conjectures such as the hardness of prime factorisation to provide security against eavesdropping attacks. Remarkably, quantum key distribution protocols like the one proposed by Bennett and Brassard provide information-theoretic security against such attacks, a much stronger form of security unreachable by classical means. However, quantum protocols realised so far are subject to a new class of attacks exploiting implementation defects in the physical devices involved, as demonstrated in numerous ingenious experiments. Following the pioneering work of Ekert proposing the use of entanglement to bound an adversary's information from Bell's theorem, we present here the experimental realisation of a complete quantum key distribution protocol immune to these vulnerabilities. We achieve this by combining theoretical developments on finite-statistics analysis, error correction, and privacy amplification, with an event-ready scheme enabling the rapid generation of high-fidelity entanglement between two trapped-ion qubits connected by an optical fibre link. The secrecy of our key is guaranteed device-independently: it is based on the validity of quantum theory, and certified by measurement statistics observed during the experiment. Our result shows that provably secure cryptography with real-world devices is possible, and paves the way for further quantum information applications based on the device-independence principle.Comment: 5+1 pages in main text and methods with 4 figures and 1 table; 37 pages of supplementary materia

    HDAC inhibitor-dependent transcriptome and memory reinstatement in cognitive decline models.

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    Aging and increased amyloid burden are major risk factors for cognitive diseases such as Alzheimer's disease (AD). Effective therapies for these diseases are lacking. Here, we evaluated mouse models of age-associated memory impairment and amyloid deposition to study transcriptome and cell type-specific epigenome plasticity in the brain and peripheral organs. We determined that aging and amyloid pathology are associated with inflammation and impaired synaptic function in the hippocampal CA1 region as the result of epigenetic-dependent alterations in gene expression. In both amyloid and aging models, inflammation was associated with increased gene expression linked to a subset of transcription factors, while plasticity gene deregulation was differentially mediated. Amyloid pathology impaired histone acetylation and decreased expression of plasticity genes, while aging altered H4K12 acetylation-linked differential splicing at the intron-exon junction in neurons, but not nonneuronal cells. Furthermore, oral administration of the clinically approved histone deacetylase inhibitor vorinostat not only restored spatial memory, but also exerted antiinflammatory action and reinstated epigenetic balance and transcriptional homeostasis at the level of gene expression and exon usage. This study provides a systems-level investigation of transcriptome plasticity in the hippocampal CA1 region in aging and AD models and suggests that histone deacetylase inhibitors should be further explored as a cost-effective therapeutic strategy against age-associated cognitive decline

    A fluorescence temperature-jump study of conformational transitions in myosin subfragment 1.

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    The tryptophan fluorescence of unmodified myosin subfragment 1 (S1) from rabbit and chicken skeletal muscle with various nucleotides and phosphate analogues bound was measured after rapid temperature jumps. The fluorescence decreased during the temperature rise. Under some conditions, this decrease was followed by an increase, reflecting structural transitions within the protein. With adenosine 5'-[beta,gamma-imido]triphosphate (p[NH]ppA) or with ADP and BeF(x) bound, this rise was very rapid (reciprocal time constant approx. 2000 s(-1)) and varied only slightly with starting temperature, suggesting that, with these ligands, two different protein conformations were present in rapid equilibrium over a large temperature range. In the presence of ATP, the transient included several relaxation processes. Overall, the results suggest that complexes of S1 with ATP or with a number of other ligands exist as a mixture of two forms in temperature-dependent equilibrium. The results throw light on the finding of different forms of S1 in recent crystallographic studies and indicate a surprising lack of strong coupling between myosin's structural state and the nature of the nucleotide bound
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