Modeling of Dislocation Structures in Materials

A phenomenological model of the evolution of an ensemble of interacting dislocations in an isotropic elastic medium is formulated. The line-defect microstructure is described in terms of a spatially coarse-grained order parameter, the dislocation density tensor. The tensor field satisfies a conservation law that derives from the conservation of Burgers vector. Dislocation motion is entirely dissipative and is assumed to be locally driven by the minimization of plastic free energy. We first outline the method and resulting equations of motion to linear order in the dislocation density tensor, obtain various stationary solutions, and give their geometric interpretation. The coupling of the dislocation density to an externally imposed stress field is also addressed, as well as the impact of the field on the stationary solutions.Comment: RevTeX, 19 pages. Also at http://www.scri.fsu.edu/~vinals/jeff1.p

Accelerating Sequence Alignments Based on FM-Index Using the Intel KNL Processor

FM-index is a compact data structure suitable for fast matches of short reads to large reference genomes. The matching algorithm using this index exhibits irregular memory access patterns that cause frequent cache misses, resulting in a memory bound problem. This paper analyzes different FM-index versions presented in the literature, focusing on those computing aspects related to the data access. As a result of the analysis, we propose a new organization of FM-index that minimizes the demand for memory bandwidth, allowing a great improvement of performance on processors with high-bandwidth memory, such as the second-generation Intel Xeon Phi (Knights Landing, or KNL), integrating ultra high-bandwidth stacked memory technology. As the roofline model shows, our implementation reaches 95% of the peak random access bandwidth limit when executed on the KNL and almost all the available bandwidth when executed on other Intel Xeon architectures with conventional DDR memory. In addition, the obtained throughput in KNL is much higher than the results reported for GPUs in the literature. IEE

Large-scale production of somatic embryos as a source of hypocotyl explants for Vitis vinifera micrografting

To the standard methods currently used to make grapevine virus-free, apex micrografting on hypocotyls of somatic embryos is proposed as an alternative procedure. The study defines optimal conditions to produce hypocotyl fragments suitable for micrografting. Interruption of the process by storage of tissues or embryos at low temperature (+ 4 °C) was assessed at different stages and for durations up to 6 months. Best procedure to produce somatic embryos were: long-term maintenance of embryogenic cultures on C1 medium (5 μM 2.4-D + 1 μM BAP, solidified with 4 g·l-1 agar and 4 g·l-1 Phytagel) ; differentiation of embryogenic callus for 2 months on C2 medium (5 μM NOA + 1 μM BAP, gelling agents same as above) ; transfer of single embryos on plant growth regulator-free medium for 2-3 weeks for germination. At different steps of the process, embryogenic tissues or differentiated embryos can be stored for up to 180 d for some cultivars. Micrografting assays were performed with various types of embryo and with apices from several V. vinifera cultivars. White to slightly coloured hypocotyls, excised from embryos germinated in darkness, gave best results for micrografting, while hypocotyl shape had little influence. For all genotypes tested the success rate ranged from 18 to 30 %.

Fate of Zero-Temperature Ising Ferromagnets

We investigate the relaxation of homogeneous Ising ferromagnets on finite lattices with zero-temperature spin-flip dynamics. On the square lattice, a frozen two-stripe state is apparently reached approximately 1/4 of the time, while the ground state is reached otherwise. The asymptotic relaxation is characterized by two distinct time scales, with the longer stemming from the influence of a long-lived diagonal stripe ``defect''. In greater than two dimensions, the probability to reach the ground state rapidly vanishes as the size increases and the system typically ends up wandering forever within an iso-energy set of stochastically ``blinking'' metastable states.Comment: 4 pages in column format, 6 figure

Square Patterns and Quasi-patterns in Weakly Damped Faraday Waves

Pattern formation in parametric surface waves is studied in the limit of weak viscous dissipation. A set of quasi-potential equations (QPEs) is introduced that admits a closed representation in terms of surface variables alone. A multiscale expansion of the QPEs reveals the importance of triad resonant interactions, and the saturating effect of the driving force leading to a gradient amplitude equation. Minimization of the associated Lyapunov function yields standing wave patterns of square symmetry for capillary waves, and hexagonal patterns and a sequence of quasi-patterns for mixed capillary-gravity waves. Numerical integration of the QPEs reveals a quasi-pattern of eight-fold symmetry in the range of parameters predicted by the multiscale expansion.Comment: RevTeX, 11 pages, 8 figure

Numerical study of pattern formation following a convective instability in non-Boussinesq fluids

We present a numerical study of a model of pattern formation following a convective instability in a non-Boussinesq fluid. It is shown that many of the features observed in convection experiments conducted on $CO_{2}$ gas can be reproduced by using a generalized two-dimensional Swift-Hohenberg equation. The formation of hexagonal patterns, rolls and spirals is studied, as well as the transitions and competition among them. We also study nucleation and growth of hexagonal patterns and find that the front velocity in this two dimensional model is consistent with the prediction of marginal stability theory for one dimensional fronts.Comment: 9 pages, report FSU-SCRI-92-6

Noise and dynamical pattern selection

In pattern forming systems such as Rayleigh-Benard convection or directional solidification, a large number of linearly stable, patterned steady states exist when the basic, simple steady state is unstable. Which of these steady states will be realized in a given experiment appears to depend on unobservable details of the system's initial conditions. We show, however, that weak, Gaussian white noise drives such a system toward a preferred wave number which depends only on the system parameters and is independent of initial conditions. We give a prescription for calculating this wave number, analytically near the onset of instability and numerically otherwise.Comment: 12 pages, REVTEX, no figures. Submitted to Phys. Rev. Let

Numerical Confirmation of Late-time t^{1/2} Growth in Three-dimensional Phase Ordering

Results for the late-time regime of phase ordering in three dimensions are reported, based on numerical integration of the time-dependent Ginzburg-Landau equation with nonconserved order parameter at zero temperature. For very large systems ($700^3$) at late times, $t \ge 150,$ the characteristic length grows as a power law, $R(t) \sim t^n$, with the measured $n$ in agreement with the theoretically expected result $n=1/2$ to within statistical errors. In this time regime $R(t)$ is found to be in excellent agreement with the analytical result of Ohta, Jasnow, and Kawasaki [Phys. Rev. Lett. {\bf 49}, 1223 (1982)]. At early times, good agreement is found between the simulations and the linearized theory with corrections due to the lattice anisotropy.Comment: Substantially revised and enlarged, submitted to PR

Sand in the wheels, or oiling the wheels, of international finance? : New Labour's appeal to a 'new Bretton Woods'

Tony Blair’s political instinct typically is to associate himself only with the future. As such, his explicit appeal to ‘the past’ in his references to New Labour’s desire to establish a “new Bretton Woods” is sufficient in itself to arouse some degree of analytical curiosity (see Blair 1998a). The fact that this appeal was made specifically in relation to Bretton Woods is even more interesting. The resonant image of the international economic context established by the original Bretton Woods agreements invokes a style and content of policy-making which Tony Blair typically dismisses as neither economically nor politically consistent with his preferred vision of the future (see Blair 2000c, 2001b)

Winding number instability in the phase-turbulence regime of the Complex Ginzburg-Landau Equation

We give a statistical characterization of states with nonzero winding number in the Phase Turbulence (PT) regime of the one-dimensional Complex Ginzburg-Landau equation. We find that states with winding number larger than a critical one are unstable, in the sense that they decay to states with smaller winding number. The transition from Phase to Defect Turbulence is interpreted as an ergodicity breaking transition which occurs when the range of stable winding numbers vanishes. Asymptotically stable states which are not spatio-temporally chaotic are described within the PT regime of nonzero winding number.Comment: 4 pages,REVTeX, including 4 Figures. Latex (or postscript) version with figures available at http://formentor.uib.es/~montagne/textos/nupt