1,286 research outputs found

    Technical note: Simulating chemical systems in Fortran90 and Matlab with the Kinetic PreProcessor KPP-2.1

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    International audienceThis paper presents the new version 2.1 of the Kinetic PreProcessor (KPP). Taking a set of chemical reactions and their rate coefficients as input, KPP generates Fortran90, Fortran77, Matlab, or C code for the temporal integration of the kinetic system. Efficiency is obtained by carefully exploiting the sparsity structures of the Jacobian and of the Hessian. A comprehensive suite of stiff numerical integrators is also provided. Moreover, KPP can be used to generate the tangent linear model, as well as the continuous and discrete adjoint models of the chemical system

    Exact and Asymptotic Measures of Multipartite Pure State Entanglement

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    In an effort to simplify the classification of pure entangled states of multi (m) -partite quantum systems, we study exactly and asymptotically (in n) reversible transformations among n'th tensor powers of such states (ie n copies of the state shared among the same m parties) under local quantum operations and classical communication (LOCC). With regard to exact transformations, we show that two states whose 1-party entropies agree are either locally-unitarily (LU) equivalent or else LOCC-incomparable. In particular we show that two tripartite Greenberger-Horne-Zeilinger (GHZ) states are LOCC-incomparable to three bipartite Einstein-Podolsky-Rosen (EPR) states symmetrically shared among the three parties. Asymptotic transformations result in a simpler classification than exact transformations. We show that m-partite pure states having an m-way Schmidt decomposition are simply parameterizable, with the partial entropy across any nontrivial partition representing the number of standard ``Cat'' states (|0^m>+|1^m>) asymptotically interconvertible to the state in question. For general m-partite states, partial entropies across different partitions need not be equal, and since partial entropies are conserved by asymptotically reversible LOCC operations, a multicomponent entanglement measure is needed, with each scalar component representing a different kind of entanglement, not asymptotically interconvertible to the other kinds. In particular the m=4 Cat state is not isentropic to, and therefore not asymptotically interconvertible to, any combination of bipartite and tripartite states shared among the four parties. Thus, although the m=4 cat state can be prepared from bipartite EPR states, the preparation process is necessarily irreversible, and remains so even asymptotically.Comment: 13 pages including 3 PostScript figures. v3 has updated references and discussion, to appear Phys. Rev.

    Optical matrix elements in tight-binding models with overlap

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    We investigate the effect of orbital overlap on optical matrix elements in empirical tight-binding models. Empirical tight-binding models assume an orthogonal basis of (atomiclike) states and a diagonal coordinate operator which neglects the intra-atomic part. It is shown that, starting with an atomic basis which is not orthogonal, the orthogonalization process induces intra-atomic matrix elements of the coordinate operator and extends the range of the effective Hamiltonian. We analyze simple tight-binding models and show that non-orthogonality plays an important role in optical matrix elements. In addition, the procedure gives formal justification to the nearest-neighbor spin-orbit interaction introduced by Boykin [Phys. Rev \textbf{B} 57, 1620 (1998)] in order to describe the Dresselahaus term which is neglected in empirical tight-binding models.Comment: 16 pages 6 figures, to appear in Phys. Rev.

    Parallel Load Balancing Strategies for Ensembles of Stochastic Biochemical Simulations

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    The evolution of biochemical systems where some chemical species are present with only a small number of molecules, is strongly influenced by discrete and stochastic effects that cannot be accurately captured by continuous and deterministic models. The budding yeast cell cycle provides an excellent example of the need to account for stochastic effects in biochemical reactions. To obtain statistics of the cell cycle progression, a stochastic simulation algorithm must be run thousands of times with different initial conditions and parameter values. In order to manage the computational expense involved, the large ensemble of runs needs to be executed in parallel. The CPU time for each individual task is unknown before execution, so a simple strategy of assigning an equal number of tasks per processor can lead to considerable work imbalances and loss of parallel efficiency. Moreover, deterministic analysis approaches are ill suited for assessing the effectiveness of load balancing algorithms in this context. Biological models often require stochastic simulation. Since generating an ensemble of simulation results is computationally intensive, it is important to make efficient use of computer resources. This paper presents a new probabilistic framework to analyze the performance of dynamic load balancing algorithms when applied to large ensembles of stochastic biochemical simulations. Two particular load balancing strategies (point-to-point and all-redistribution) are discussed in detail. Simulation results with a stochastic budding yeast cell cycle model confirm the theoretical analysis. While this work is motivated by cell cycle modeling, the proposed analysis framework is general and can be directly applied to any ensemble simulation of biological systems where many tasks are mapped onto each processor, and where the individual compute times vary considerably among tasks

    Violations of local realism by two entangled quNits

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    Results obtained in two recent papers, \cite{Kaszlikowski} and \cite{Durt}, seem to indicate that the nonlocal character of the correlations between the outcomes of measurements performed on entangled systems separated in space is not robust in the presence of noise. This is surprising, since entanglement itself is robust. Here we revisit this problem and argue that the class of gedanken-experiments considered in \cite{Kaszlikowski} and \cite{Durt} is too restrictive. By considering a more general class, involving sequences of measurements, we prove that the nonlocal correlations are in fact robust.Comment: Reference added, 3 pages, accepted for publication in J. Phys. A: Math. and Genera

    Anisotropic magnetoresistance of bulk carbon nanotube sheets

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    We have measured the magnetoresistance of stretched sheets of carbon nanotubes in temperatures ranging from 2 K to 300 K and in magnetic fields up to 9 T, oriented either perpendicular or parallel to the plane of the sheets. The samples have been partially aligned by post-fabrication stretching, such that the direction of stretching was either parallel or perpendicular to the direction of applied electric current. We have observed large differences between the magnetoresistance measured under the two field orientations, most pronounced at the lowest temperatures, highest fields, and for the laterally-aligned sample. Treatment of the sheets with nitric acid affects this anisotropy. We analyzed the results within the theoretical framework of weak and strong localization and concluded that the anisotropy bears the mark of a more unusual phenomenon, possibly magnetically-induced mechanical strain.Comment: 34 pages, 10 figure

    High Temperature Mixed State cc-Axis Dissipation in Low Carrier Density Y0.54Pr0.46Ba2Cu3O7δY_{0.54}Pr_{0.46}Ba_{2}Cu_{3}O_{7-\delta}

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    The nature of the out-of-plane dissipation was investigated in underdoped Y0.54Pr0.46Ba2Cu3O7δY_{0.54}Pr_{0.46}Ba_{2}Cu_{3}O_{7-\delta} single crystals at temperatures close to the critical temperature. For this goal, temperature and angle dependent out-of-plane resistivity measurements were carried out both below and above the critical temperature. We found that the Ambegaokar-Halperin relationship [V. Ambegaokar, and B. I. Halperin, Phys. Rev. Lett. \textbf{22}, 1364 (1969)] depicts very well the angular magnetoresistivity in the investigated range of field and temperature. The main finding is that the in-plane phase fluctuations decouple the layers above the critical temperature and the charge transport is governed only by the quasiparticles. We also have calculated the interlayer Josephson critical current density, which was found to be much smaller than the one predicted by the theory of layered superconductors. This discrepancy could be a result of the d-wave symmetry of the order parameter and/or of the non BCS temperature dependence of the c-axis penetration length.Comment: Will appear in PR
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