Gene-network inference by message passing

The inference of gene-regulatory processes from gene-expression data belongs to the major challenges of computational systems biology. Here we address the problem from a statistical-physics perspective and develop a message-passing algorithm which is able to infer sparse, directed and combinatorial regulatory mechanisms. Using the replica technique, the algorithmic performance can be characterized analytically for artificially generated data. The algorithm is applied to genome-wide expression data of baker's yeast under various environmental conditions. We find clear cases of combinatorial control, and enrichment in common functional annotations of regulated genes and their regulators.Comment: Proc. of International Workshop on Statistical-Mechanical Informatics 2007, Kyot

Gene-network inference by message passing

The inference of gene-regulatory processes from gene-expression data belongs to the major challenges of computational systems biology. Here we address the problem from a statistical-physics perspective and develop a message-passing algorithm which is able to infer sparse, directed and combinatorial regulatory mechanisms. Using the replica technique, the algorithmic performance can be characterized analytically for artificially generated data. The algorithm is applied to genome-wide expression data of baker's yeast under various environmental conditions. We find clear cases of combinatorial control, and enrichment in common functional annotations of regulated genes and their regulators.Comment: Proc. of International Workshop on Statistical-Mechanical Informatics 2007, Kyot

Gene-network inference by message passing

The inference of gene-regulatory processes from gene-expression data belongs to the major challenges of computational systems biology. Here we address the problem from a statistical-physics perspective and develop a message-passing algorithm which is able to infer sparse, directed and combinatorial regulatory mechanisms. Using the replica technique, the algorithmic performance can be characterized analytically for artificially generated data. The algorithm is applied to genome-wide expression data of baker's yeast under various environmental conditions. We find clear cases of combinatorial control, and enrichment in common functional annotations of regulated genes and their regulators.Comment: Proc. of International Workshop on Statistical-Mechanical Informatics 2007, Kyot

Universal cloning of continuous quantum variables

The cloning of quantum variables with continuous spectra is analyzed. A universal - or Gaussian - quantum cloning machine is exhibited that copies equally well the states of two conjugate variables such as position and momentum. It also duplicates all coherent states with a fidelity of 2/3. More generally, the copies are shown to obey a no-cloning Heisenberg-like uncertainty relation.Comment: 4 pages, RevTex. Minor revisions, added explicit cloning transformation, added reference

Multipartite entanglement for continuous variables: A quantum teleportation network

We show that {\it one} single-mode squeezed state distributed among $N$ parties using linear optics suffices to produce a truly $N$-partite entangled state for any nonzero squeezing and arbitrarily many parties. From this $N$-partite entangled state, via quadrature measurements of $N-2$ modes, bipartite entanglement between any two of the $N$ parties can be `distilled', which enables quantum teleportation with an experimentally determinable fidelity better than could be achieved in any classical scheme.Comment: 4 pages, 2 figures, published version, paper shorter, title longe

Broadband teleportation

Quantum teleportation of an unknown broadband electromagnetic field is investigated. The continuous-variable teleportation protocol by Braunstein and Kimble [Phys. Rev. Lett. {\bf 80}, 869 (1998)] for teleporting the quantum state of a single mode of the electromagnetic field is generalized for the case of a multimode field with finite bandwith. We discuss criteria for continuous-variable teleportation with various sets of input states and apply them to the teleportation of broadband fields. We first consider as a set of input fields (from which an independent state preparer draws the inputs to be teleported) arbitrary pure Gaussian states with unknown coherent amplitude (squeezed or coherent states). This set of input states, further restricted to an alphabet of coherent states, was used in the experiment by Furusawa {\it et al.} [Science {\bf 282}, 706 (1998)]. It requires unit-gain teleportation for optimizing the teleportation fidelity. In our broadband scheme, the excess noise added through unit-gain teleportation due to the finite degree of the squeezed-state entanglement is just twice the (entanglement) source's squeezing spectrum for its ``quiet quadrature.'' The teleportation of one half of an entangled state (two-mode squeezed vacuum state), i.e., ``entanglement swapping,'' and its verification are optimized under a certain nonunit gain condition. We will also give a broadband description of this continuous-variable entanglement swapping based on the single-mode scheme by van Loock and Braunstein [Phys. Rev. A {\bf 61}, 10302 (2000)]Comment: 27 pages, 7 figures, revised version for publication, Physical Review A (August 2000); major changes, in parts rewritte

Synchronization in Scale Free networks: The role of finite size effects

Synchronization problems in complex networks are very often studied by researchers due to its many applications to various fields such as neurobiology, e-commerce and completion of tasks. In particular, Scale Free networks with degree distribution $P(k)\sim k^{-\lambda}$, are widely used in research since they are ubiquitous in nature and other real systems. In this paper we focus on the surface relaxation growth model in Scale Free networks with $2.5< \lambda <3$, and study the scaling behavior of the fluctuations, in the steady state, with the system size $N$. We find a novel behavior of the fluctuations characterized by a crossover between two regimes at a value of $N=N^*$ that depends on $\lambda$: a logarithmic regime, found in previous research, and a constant regime. We propose a function that describes this crossover, which is in very good agreement with the simulations. We also find that, for a system size above $N^{*}$, the fluctuations decrease with $\lambda$, which means that the synchronization of the system improves as $\lambda$ increases. We explain this crossover analyzing the role of the network's heterogeneity produced by the system size $N$ and the exponent of the degree distribution.Comment: 9 pages and 5 figures. Accepted in Europhysics Letter

Entangling two distant nanocavities via a waveguide

In this paper, we investigate the generation of continuous variable entanglement between two spatially-separate nanocavities mediated by a coupled resonator optical waveguide in photonic crystals. By solving the exact dynamics of the cavity system coupled to the waveguide, the entanglement and purity of the two-mode cavity state are discussed in detail for the initially separated squeezing inputs. It is found that the stable and pure entangled state of the two distant nanocavities can be achieved with the requirement of only a weak cavity-waveguide coupling when the cavities are resonant with the band center of the waveguide. The strong couplings between the cavities and the waveguide lead to the entanglement sudden death and sudden birth. When the frequencies of the cavities lie outside the band of the waveguide, the waveguide-induced cross frequency shift between the cavities can optimize the achievable entanglement. It is also shown that the entanglement can be easily manipulated through the changes of the cavity frequencies within the waveguide band.Comment: 8 pages, 8 figure

Quantum Communication with Correlated Nonclassical States

Nonclassical correlations between the quadrature-phase amplitudes of two spatially separated optical beams are exploited to realize a two-channel quantum communication experiment with a high degree of immunity to interception. For this scheme, either channel alone can have an arbitrarily small signal-to-noise ratio (SNR) for transmission of a coherent ``message''. However, when the transmitted beams are combined properly upon authorized detection, the encoded message can in principle be recovered with the original SNR of the source. An experimental demonstration has achieved a 3.2 dB improvement in SNR over that possible with correlated classical sources. Extensions of the protocol to improve its security against eavesdropping are discussed.Comment: 8 pages and 4 figures (Figure 1; Figures 2a, 2b; Figure 2

Quantum Dense Coding Exploiting Bright EPR Beam

Highly efficient quantum dense coding for continuous variables has been experimentally accomplished by means of exploiting bright EPR beam with anticorrelation of amplitude quadratures and correlation of phase quadratures, which is generated from a nondegenerate optical parametric amplifier operating in the state of deamplification. Two bits of classical information are encoded on two quadratures of a half of bright EPR beam at the sender Alice and transmitted to the receiver Bob via one qubit of the shared quantum state after encoding. The amplitude and phase signals are simultaneously decoded with the other half of EPR beam by the direct measurement of the Bell-state at Bob. The signal to noise ratios of the simultaneously measured amplitude and phase signals are improved 5.4dB and 4.8dB with respect to that of the shot noise limit respectively. A high degree of immunity to unauthorized eavesdropping of the presented quantum communication scheme is experimentally demonstrated.Comment: 11 pages, 5 figure