238 research outputs found
Matrix controlled channel diffusion of sodium in amorphous silica
To find the origin of the diffusion channels observed in sodium-silicate
glasses, we have performed classical molecular dynamics simulations of
NaO--4SiO during which the mass of the Si and O atoms has been
multiplied by a tuning coefficient. We observe that the channels disappear and
that the diffusive motion of the sodium atoms vanishes if this coefficient is
larger than a threshold value. Above this threshold the vibrational states of
the matrix are not compatible with those of the sodium ions. We interpret hence
the decrease of the diffusion by the absence of resonance conditions.Comment: 5 pages, 4 figure
Metastable Dynamics above the Glass Transition
The element of metastability is incorporated in the fluctuating nonlinear
hydrodynamic description of the mode coupling theory (MCT) of the liquid-glass
transition. This is achieved through the introduction of the defect density
variable into the set of slow variables with the mass density and
the momentum density . As a first approximation, we consider the case
where motions associated with are much slower than those associated with
. Self-consistently, assuming one is near a critical surface in the MCT
sense, we find that the observed slowing down of the dynamics corresponds to a
certain limit of a very shallow metastable well and a weak coupling between
and . The metastability parameters as well as the exponents
describing the observed sequence of time relaxations are given as smooth
functions of the temperature without any evidence for a special temperature. We
then investigate the case where the defect dynamics is included. We find that
the slowing down of the dynamics corresponds to the system arranging itself
such that the kinetic coefficient governing the diffusion of the
defects approaches from above a small temperature-dependent value .Comment: 38 pages, 14 figures (6 figs. are included as a uuencoded tar-
compressed file. The rest is available upon request.), RevTEX3.0+eps
Introducing EMMIE: An evidence rating scale to encourage mixed-method crime prevention synthesis reviews
Objectives This short report describes the need for, and the development of, a coding system to distil the quality and coverage of systematic reviews of the evidence relating to crime prevention interventions. The starting point for the coding system concerns the evidence needs of policymakers and practitioners. Methods The coding scheme (EMMIE) proposed builds on previous scales that have been developed to assess the probity, coverage and utility of evidence both in health and criminal justice. It also draws on the principles of realist synthesis and review. Results The proposed EMMIE scale identifies five dimensions to which systematic reviews intended to inform crime prevention should speak. These are the Effect of intervention, the identification of the causal Mechanism(s) through which interventions are intended to work, the factors that Moderate their impact, the articulation of practical Implementation issues, and the Economic costs of intervention
Conformational and Structural Relaxations of Poly(ethylene oxide) and Poly(propylene oxide) Melts: Molecular Dynamics Study of Spatial Heterogeneity, Cooperativity, and Correlated Forward-Backward Motion
Performing molecular dynamics simulations for all-atom models, we
characterize the conformational and structural relaxations of poly(ethylene
oxide) and poly(propylene oxide) melts. The temperature dependence of these
relaxation processes deviates from an Arrhenius law for both polymers. We
demonstrate that mode-coupling theory captures some aspects of the glassy
slowdown, but it does not enable a complete explanation of the dynamical
behavior. When the temperature is decreased, spatially heterogeneous and
cooperative translational dynamics are found to become more important for the
structural relaxation. Moreover, the transitions between the conformational
states cease to obey Poisson statistics. In particular, we show that, at
sufficiently low temperatures, correlated forward-backward motion is an
important aspect of the conformational relaxation, leading to strongly
nonexponential distributions for the waiting times of the dihedrals in the
various conformational statesComment: 13 pages, 13 figure
A haplotype map of allohexaploid wheat reveals distinct patterns of selection on homoeologous genomes
Citation: Jordan, K. W., Wang, S., Lun, Y., Gardiner, L. J., MacLachlan, R., Hucl, P., . . . Akhunov, E. (2015). A haplotype map of allohexaploid wheat reveals distinct patterns of selection on homoeologous genomes. Genome Biology, 16(1).
https://doi.org/10.1186/s13059-015-0606-4Background: Bread wheat is an allopolyploid species with a large, highly repetitive genome. To investigate the impact of selection on variants distributed among homoeologous wheat genomes and to build a foundation for understanding genotype-phenotype relationships, we performed population-scale re-sequencing of a diverse panel of wheat lines. Results: A sample of 62 diverse lines was re-sequenced using the whole exome capture and genotyping-by-sequencing approaches. We describe the allele frequency, functional significance, and chromosomal distribution of 1.57 million single nucleotide polymorphisms and 161,719 small indels. Our results suggest that duplicated homoeologous genes are under purifying selection. We find contrasting patterns of variation and inter-variant associations among wheat genomes; this, in addition to demographic factors, could be explained by differences in the effect of directional selection on duplicated homoeologs. Only a small fraction of the homoeologous regions harboring selected variants overlapped among the wheat genomes in any given wheat line. These selected regions are enriched for loci associated with agronomic traits detected in genome-wide association studies. Conclusions: Evidence suggests that directional selection in allopolyploids rarely acted on multiple parallel advantageous mutations across homoeologous regions, likely indicating that a fitness benefit could be obtained by a mutation at any one of the homoeologs. Additional advantageous variants in other homoelogs probably either contributed little benefit, or were unavailable in populations subjected to directional selection. We hypothesize that allopolyploidy may have increased the likelihood of beneficial allele recovery by broadening the set of possible selection targets. © 2015 Jordan et al.; licensee BioMed Central.Additional Authors: Talbert, L.;Bansal, U. K.;Bariana, H. S.;Hayden, M. J.;Pozniak, C.;Jeddeloh, J. A.;Hall, A
Broadband Dielectric Spectroscopy on Glass-Forming Propylene Carbonate
Dielectric spectroscopy covering more than 18 decades of frequency has been
performed on propylene carbonate in its liquid and supercooled-liquid state.
Using quasi-optic submillimeter and far-infrared spectroscopy the dielectric
response was investigated up to frequencies well into the microscopic regime.
We discuss the alpha-process whose characteristic timescale is observed over 14
decades of frequency and the excess wing showing up at frequencies some three
decades above the peak frequency. Special attention is given to the
high-frequency response of the dielectric loss in the crossover regime between
alpha-peak and boson-peak. Similar to our previous results in other glass
forming materials we find evidence for additional processes in the crossover
regime. However, significant differences concerning the spectral form at high
frequencies are found. We compare our results to the susceptibilities obtained
from light scattering and to the predictions of various models of the glass
transition.Comment: 13 pages, 9 figures, submitted to Phys. Rev.
Metastable Dynamics of the Hard-Sphere System
The reformulation of the mode-coupling theory (MCT) of the liquid-glass
transition which incorporates the element of metastability is applied to the
hard-sphere system. It is shown that the glass transition in this system is not
a sharp one at the special value of the density or the packing fraction, which
is in contrast to the prediction by the conventional MCT. Instead we find that
the slowing down of the dynamics occurs over a range of values of the packing
fraction. Consequently, the exponents governing the sequence of time
relaxations in the intermediate time regime are given as functions of packing
fraction with one additional parameter which describes the overall scale of the
metastable potential energy for defects in the hard-sphere system. Implications
of the present model on the recent experiments on colloidal systems are also
discussed.Comment: 21 pages, 5 figures (available upon request), RevTEX3.0, JFI
Preprint
Isomorph invariance of the structure and dynamics of classical crystals
This paper shows by computer simulations that some crystalline systems have
curves in their thermodynamic phase diagrams, so-called isomorphs, along which
structure and dynamics in reduced units are invariant to a good approximation.
The crystals are studied in a classical-mechanical framework, which is
generally a good description except significantly below melting. The existence
of isomorphs for crystals is validated by simulations of particles interacting
via the Lennard-Jones pair potential arranged into a face-centered cubic (FCC)
crystalline structure; the slow vacancy-jump dynamics of a defective FCC
crystal is also shown to be isomorph invariant. In contrast, a NaCl crystal
model does not exhibit isomorph invariances. Other systems simulated, though in
less detail, are the Wahnstrom binary Lennard-Jones crystal with the Laves crystal structure, monatomic FCC crystals of particles
interacting via the Buckingham pair potential and via a novel purely repulsive
pair potential diverging at a finite separation, an ortho-terphenyl molecular
model, and SPC/E hexagonal ice. Except for NaCl and ice, the crystals simulated
all have isomorphs. Based on these findings and previous simulations of liquid
models, we conjecture that crystalline solids with isomorphs include most or
all formed by atoms or molecules interacting via metallic or van der Waals
forces, whereas covalently- or hydrogen-bonded crystals are not expected to
have isomorphs. Crystals of ions or dipolar molecules constitute a limiting
case for which isomorphs are only expected when the Coulomb interactions are
relatively weak. We briefly discuss the consequences of the findings for
theories of melting and crystallization
Novel octaketide macrolides related to 6-deoxyerythronolide B provide evidence for iterative operation of the erythromycin polyketide synthase
AbstractBackground: The macrolide antibiotic erythromycin A, like other complex aliphatic polyketides, is synthesised by a bacterial modular polyketide synthase (PKS). Such PKSs, in contrast to other fatty acid and polyketide synthases which work iteratively, contain a separate set or module of enzyme activities for each successive cycle of polyketide chain extension, and the number and type of modules together determine the structure of the polyketide product. Thus, the six extension modules of the erythromycin PKS (DEBS) together catalyse the production of the specific heptaketide 6-deoxyerythronolide B.Results: A mutant strain of the erythromycin producer Saccharopolyspora erythraea, which accumulates the aglycone intermediate erythronolide B, was found unexpectedly to produce two novel octaketides, both 16-membered macrolides. These compounds were detectable in fermentation broths of wild-type S. erythraea, but not in a strain from which the DEBS genes had been specifically deleted. From their structures, both of these octaketides appear to be aberrant products of DEBS in which module 4 has âstutteredâ, that is, has catalysed two successive cycles of chain extension.Conclusions: The isolation of novel DEBS-derived octaketides provides the first evidence that an extension module in a modular PKS has the potential to catalyse iterative rounds of chain elongation like other type I FAS and PKS systems. The factors governing the extent of such âstutteringâ remain to be determined
Static and Dynamic Properties of a Viscous Silica Melt Molecular Dynamics Computer Simulations
We present the results of a large scale molecular dynamics computer
simulation in which we investigated the static and dynamic properties of a
silica melt in the temperature range in which the viscosity of the system
changes from O(10^-2) Poise to O(10^2) Poise. We show that even at temperatures
as high as 4000 K the structure of this system is very similar to the random
tetrahedral network found in silica at lower temperatures. The temperature
dependence of the concentration of the defects in this network shows an
Arrhenius law. From the partial structure factors we calculate the neutron
scattering function and find that it agrees very well with experimental neutron
scattering data. At low temperatures the temperature dependence of the
diffusion constants shows an Arrhenius law with activation energies which
are in very good agreement with the experimental values. With increasing
temperature we find that this dependence shows a cross-over to one which can be
described well by a power-law, D\propto (T-T_c)^gamma. The critical temperature
T_c is 3330 K and the exponent gamma is close to 2.1. Since we find a similar
cross-over in the viscosity we have evidence that the relaxation dynamics of
the system changes from a flow-like motion of the particles, as described by
the ideal version of mode-coupling theory, to a hopping like motion. We show
that such a change of the transport mechanism is also observed in the product
of the diffusion constant and the life time of a Si-O bond, or the space and
time dependence of the van Hove correlation functions.Comment: 30 pages of Latex, 14 figure
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