8,479 research outputs found
Interaction of Nucleosides and Related Compounds with Nucleic Acids as Indicated by the Change of Helix-Coil Transition Temperature
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°
The dune-subgrid module and some applications
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
Polyhedral GauĂź-Seidel converges
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
Truncated nonsmooth Newton multigrid methods for simplex-constrained minimization problems
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
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
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)
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The interface for functions in the dune-functions module
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
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
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°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°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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