7,918 research outputs found

    Interaction of Nucleosides and Related Compounds with Nucleic Acids as Indicated by the Change of Helix-Coil Transition Temperature

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    A series of compounds has been tested for effectiveness in lowering the melting temperature of poly A and of thymus DNA. The order of increasing activity was found to be: adonitol, methyl riboside (both negligible) < cyclohexanol < phenol, pyrimidine, uridine < cytidine, thymidine < purine, adenosine, inosine, deoxyguanosine < caffeine, coumarin, 2,6-dichloro-7-methylpurine. Urea was ineffective with poly A and only slightly effective with DNA. At a concentration of 0.3 M, purine lowered the Tm of DNA about 9°

    Polyhedral GauĂź-Seidel converges

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    We prove global convergence of an inexact extended polyhedral GauĂź-Seidel method for the minimization of strictly convex functionals that are continuously differentiable on each polyhedron of a polyhedral decomposition of their domains of definition. While pure GauĂź-Seidel methods are known to be very slow for problems governed by partial differential equations, the presented convergence result also covers multilevel methods that extend the GauĂź-Seidel step by coarse level corrections. Our result generalizes the proof of [10] for differentiable functionals on the Gibbs simplex. Example applications are given that require the generality of our approach

    The dune-subgrid module and some applications

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    We present an extension module for the Dune system. This module, called dune-subgrid, allows to mark elements of another Dune hierarchical grid. The set of marked elements can then be accessed as a Dune grid in its own right. dune-subgrid is free software and is available for download (External Dune Modules: www.​dune-project.​org/​downloadext.​html). We describe the functionality and use of dune-subgrid, comment on its implementation, and give two example applications. First, we show how dune-subgrid can be used for micro-FE simulations of trabecular bone. Then we present an algorithm that allows to use exact residuals for the adaptive solution of the spatial problems of time-discretized evolution equations

    Truncated nonsmooth Newton multigrid methods for simplex-constrained minimization problems

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    We present a multigrid method for the minimization of strongly convex functionals defined on a finite product of simplices. Such problems result, for example, from the discretization of multi-component phase-field problems. Our algorithm is globally convergent, requires no regularization parameters, and achieves multigrid convergence rates. We present numerical results for the vector-valued Allen--Cahn equation and observe that the convergence rate is independent from the temperature parameter and the number of components

    Formation of wind-captured discs in Supergiant X-ray binaries : consequences for Vela X-1 and Cygnus X-1

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    In Supergiant X-ray binaries (SgXB), a compact object captures a fraction of the wind of an O/B supergiant on a close orbit. Proxies exist to evaluate the efficiency of mass and angular momentum accretion but they depend so dramatically on the wind speed that given the current uncertainties, they only set loose constrains. Furthermore, they often bypass the impact of orbital and shock effects on the flow structure. We study the wind dynamics and the angular momentum gained as the flow is accreted. We identify the conditions for the formation of a disc-like structure around the accretor and the observational consequences for SgXB. We use recent results on the wind launching mechanism to compute 3D streamlines, accounting for the gravitational and X-ray ionizing influence of the compact companion on the wind. Once the flow enters the Roche lobe of the accretor, we solve the hydrodynamics equations with cooling. A shocked region forms around the accretor as the flow is beamed. For wind speeds of the order of the orbital speed, the shock is highly asymmetric compared to the axisymmetric bow shock obtained for a purely planar homogeneous flow. With net radiative cooling, the flow always circularizes for wind speeds low enough. Although the donor star does not fill its Roche lobe, the wind can be significantly beamed and bent by the orbital effects. The net angular momentum of the accreted flow is then sufficient to form a persistent disc-like structure. This mechanism could explain the proposed limited outer extension of the accretion disc in Cygnus X-1 and suggests the presence of a disc at the outer rim of the neutron star magnetosphere in Vela X-1, with dramatic consequences on the spinning up of the accretor

    Surface stress of Ni adlayers on W(110): the critical role of the surface atomic structure

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    Puzzling trends in surface stress were reported experimentally for Ni/W(110) as a function of Ni coverage. In order to explain this behavior, we have performed a density-functional-theory study of the surface stress and atomic structure of the pseudomorphic and of several different possible 1x7 configurations for this system. For the 1x7 phase, we predict a different, more regular atomic structure than previously proposed based on surface x-ray diffraction. At the same time, we reproduce the unexpected experimental change of surface stress between the pseudomorphic and 1x7 configuration along the crystallographic surface direction which does not undergo density changes. We show that the observed behavior in the surface stress is dominated by the effect of a change in Ni adsorption/coordination sites on the W(110) surface.Comment: 14 pages, 3 figures Published in J. Phys.: Condens. Matter 24 (2012) 13500

    The interface for functions in the dune-functions module

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    The dune-functions dune module introduces a new programmer interface for discrete and non-discrete functions. Unlike the previous interfaces considered in the existing dune modules, it is based on overloading operator(), and returning values by-value. This makes user code much more readable, and allows the incorporation of newer C++ features such as lambda expressions. Run-time polymorphism is implemented not by inheritance, but by type erasure, generalizing the ideas of the std::function class from the C++11 standard library. We describe the new interface, show its possibilities, and measure the performance impact of type erasure and return-by-value

    Function space bases in the dune-functions module

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    The dune-functions Dune module provides interfaces for functions and function space bases. It forms one abstraction level above grids, shape functions, and linear algebra, and provides infrastructure for full discretization frameworks like dune-pdelab and dune-fem. This document describes the function space bases provided by dune-functions. These are based on an abstract description of bases for product spaces as trees of simpler bases. From this description, many different numberings of degrees of freedom by multi-indices can be derived in a natural way. We describe the abstract concepts, document the programmer interface, and give a complete example program that solves the stationary Stokes equation using Taylor-Hood elements

    Growth modes of Fe(110) revisited: a contribution of self-assembly to magnetic materials

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    We have revisited the epitaxial growth modes of Fe on W(110) and Mo(110), and propose an overview or our contribution to the field. We show that the Stranski-Krastanov growth mode, recognized for a long time in these systems, is in fact characterized by a bimodal distribution of islands for growth temperature in the range 250-700&deg;C. We observe firstly compact islands whose shape is determined by Wulff-Kaischev's theorem, secondly thin and flat islands that display a preferred height, ie independant from nominal thickness and deposition procedure (1.4nm for Mo, and 5.5nm for W on the average). We used this effect to fabricate self-organized arrays of nanometers-thick stripes by step decoration. Self-assembled nano-ties are also obtained for nucleation of the flat islands on Mo at fairly high temperature, ie 800&deg;C. Finally, using interfacial layers and solid solutions we separate two effects on the preferred height, first that of the interfacial energy, second that of the continuously-varying lattice parameter of the growth surface.Comment: 49 pages. Invited topical review for J. Phys.: Condens. Matte
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