173 research outputs found
Anomalous Drude Model
A generalization of the Drude model is studied. On the one hand, the free
motion of the particles is allowed to be sub- or superdiffusive; on the other
hand, the distribution of the time delay between collisions is allowed to have
a long tail and even a non-vanishing first moment. The collision averaged
motion is either regular diffusive or L\'evy-flight like. The anomalous
diffusion coefficients show complex scaling laws. The conductivity can be
calculated in the diffusive regime. The model is of interest for the
phenomenological study of electronic transport in quasicrystals.Comment: 4 pages, latex, 2 figures, to be published in Physical Review Letter
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
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
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
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
Hopping Transport in the Presence of Site Energy Disorder: Temperature and Concentration Scaling of Conductivity Spectra
Recent measurements on ion conducting glasses have revealed that conductivity
spectra for various temperatures and ionic concentrations can be superimposed
onto a common master curve by an appropriate rescaling of the conductivity and
frequency. In order to understand the origin of the observed scaling behavior,
we investigate by Monte Carlo simulations the diffusion of particles in a
lattice with site energy disorder for a wide range of both temperatures and
concentrations. While the model can account for the changes in ionic activation
energies upon changing the concentration, it in general yields conductivity
spectra that exhibit no scaling behavior. However, for typical concentrations
and sufficiently low temperatures, a fairly good data collapse is obtained
analogous to that found in experiment.Comment: 6 pages, 4 figure
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
Dissecting the Effects of Concentrated Carbohydrate Solutions on Protein Diffusion, Hydration, and Internal Dynamics
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